dbSNP rs10206899: ALMS1P1:n.738-40T>C (chr2-73673773-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000755955.1(ALMS1P1):n.8T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 802,780 control chromosomes in the GnomAD database, including 25,374 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 8595 hom., cov: 28)

Exomes 𝑓: 0.21 ( 16779 hom. )

Consequence

ALMS1P1
ENST00000755955.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.783

Publications

43 publications found

Variant links:

Genes affected

ALMS1P1 (HGNC:):

ALMS1P1 links:

ALMS1P1 (HGNC:29586): (ALMS1 pseudogene 1)

ALMS1P1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000755955.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755955.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALMS1P1	NR_003683.2		n.738-40T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ALMS1P1	ENST00000450720.5	TSL:1	n.738-40T>C	intron	N/A
ALMS1P1	ENST00000755955.1		n.8T>C	non_coding_transcript_exon	Exon 1 of 2
ALMS1P1	ENST00000428767.1	TSL:6	n.550-40T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

44901

AN:

148414

Hom.:

8566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.272

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.00492

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.291

GnomAD2 exomes

AF:

0.207

AC:

32123

AN:

154944

AF XY:

0.201

show subpopulations

Gnomad AFR exome

AF:

0.566

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.00365

Gnomad FIN exome

AF:

0.188

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.203

GnomAD4 exome

AF:

0.210

AC:

137720

AN:

654274

Hom.:

16779

Cov.:

AF XY:

0.207

AC XY:

71560

AN XY:

345336

show subpopulations

African (AFR)

AF:

0.545

AC:

8823

AN:

16192

American (AMR)

AF:

0.231

AC:

7242

AN:

31302

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

3064

AN:

17836

East Asian (EAS)

AF:

0.00404

AC:

109

AN:

26950

South Asian (SAS)

AF:

0.156

AC:

10054

AN:

64328

European-Finnish (FIN)

AF:

0.183

AC:

7101

AN:

38816

Middle Eastern (MID)

AF:

0.201

AC:

559

AN:

2788

European-Non Finnish (NFE)

AF:

0.221

AC:

94260

AN:

425918

Other (OTH)

AF:

0.216

AC:

6508

AN:

30144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

5576

11151

16727

22302

27878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2014

4028

6042

8056

10070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.303

AC:

44979

AN:

148506

Hom.:

8595

Cov.:

AF XY:

0.296

AC XY:

21365

AN XY:

72178

show subpopulations

African (AFR)

AF:

0.542

AC:

21911

AN:

40442

American (AMR)

AF:

0.273

AC:

3941

AN:

14458

Ashkenazi Jewish (ASJ)

AF:

0.178

AC:

615

AN:

3458

East Asian (EAS)

AF:

0.00493

AC:

AN:

5066

South Asian (SAS)

AF:

0.139

AC:

649

AN:

4664

European-Finnish (FIN)

AF:

0.192

AC:

1841

AN:

9598

Middle Eastern (MID)

AF:

0.201

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.224

AC:

15116

AN:

67588

Other (OTH)

AF:

0.288

AC:

588

AN:

2044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1342

2685

4027

5370

6712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.248

Hom.:

4873

Bravo

AF:

0.318

Asia WGS

AF:

0.104

AC:

362

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.95

(source)

DANN

Benign

0.33

PhyloP100

-0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over