dbSNP rs16968478: ENSG00000261821:n.4276A>G (chr15-74370470-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000568496.3(ENSG00000261821):n.4276A>G 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 0.316 in 152,128 control chromosomes in the GnomAD database, including 9,638 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 0.32 ( 9635 hom., cov: 32)

Exomes 𝑓: 0.36 ( 3 hom. )

Consequence

ENSG00000261821
ENST00000568496.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

Publications

12 publications found

Variant links:

Genes affected

ENSG00000261821 (HGNC:):

ENSG00000261821 links:

Genome browser will be placed here

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 = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903524	XR_007064709.1 link	n.4853A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000261821	ENST00000568496.3 link	n.4276A>G	non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000302041	ENST00000783573.1 link	n.116-392T>C	intron_variant	Intron 1 of 1
ENSG00000302041	ENST00000783574.1 link	n.187-392T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48036

AN:

151988

Hom.:

9596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.292

GnomAD4 exome

AF:

0.364

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.316

AC:

48139

AN:

152106

Hom.:

9635

Cov.:

AF XY:

0.319

AC XY:

23694

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.560

AC:

23200

AN:

41456

American (AMR)

AF:

0.254

AC:

3880

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

880

AN:

3470

East Asian (EAS)

AF:

0.459

AC:

2380

AN:

5180

South Asian (SAS)

AF:

0.436

AC:

2102

AN:

4822

European-Finnish (FIN)

AF:

0.198

AC:

2101

AN:

10588

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12571

AN:

67982

Other (OTH)

AF:

0.297

AC:

627

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1538

3075

4613

6150

7688

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<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:

0.226

Hom.:

7722

Bravo

AF:

0.331

Asia WGS

AF:

0.474

AC:

1649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.87

(source)

DANN

Benign

0.38

PhyloP100

-0.53

Splicing

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over