dbSNP rs11006702: AIFM1P1:n.888C>T (chr10-18737678-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000413342.1(AIFM1P1):n.888C>T 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 0.251 in 339,510 control chromosomes in the GnomAD database, including 11,740 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 0.29 ( 6883 hom., cov: 32)

Exomes 𝑓: 0.22 ( 4857 hom. )

Consequence

AIFM1P1
ENST00000413342.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.245

Publications

1 publications found

Variant links:

Genes affected

AIFM1P1 (HGNC:44884): (AIFM1 pseudogene 1)

AIFM1P1 links:

ENSG00000234244 (HGNC:):

ENSG00000234244 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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
AIFM1P1		n.18737678C>T	intragenic_variant
LOC105376440	XR_930720.2 link	n.51+27317C>T	intron_variant	Intron 1 of 4
LOC105376440	XR_930721.2 link	n.69-9011C>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AIFM1P1	ENST00000413342.1 link	n.888C>T	non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000234244	ENST00000654305.2 link	n.104-9011C>T	intron_variant	Intron 1 of 2
ENSG00000234244	ENST00000654415.1 link	n.109+5232C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43474

AN:

151764

Hom.:

6866

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.189

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.251

GnomAD4 exome

AF:

0.222

AC:

41564

AN:

187630

Hom.:

4857

Cov.:

AF XY:

0.218

AC XY:

23664

AN XY:

108618

show subpopulations

African (AFR)

AF:

0.416

AC:

1538

AN:

3700

American (AMR)

AF:

0.174

AC:

2296

AN:

13166

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

625

AN:

3690

East Asian (EAS)

AF:

0.126

AC:

802

AN:

6358

South Asian (SAS)

AF:

0.167

AC:

5214

AN:

31178

European-Finnish (FIN)

AF:

0.220

AC:

2433

AN:

11082

Middle Eastern (MID)

AF:

0.143

AC:

307

AN:

2154

European-Non Finnish (NFE)

AF:

0.244

AC:

26250

AN:

107422

Other (OTH)

AF:

0.236

AC:

2099

AN:

8880

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1450

2901

4351

5802

7252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.287

AC:

43526

AN:

151880

Hom.:

6883

Cov.:

AF XY:

0.282

AC XY:

20946

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.420

AC:

17367

AN:

41364

American (AMR)

AF:

0.242

AC:

3698

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

656

AN:

3470

East Asian (EAS)

AF:

0.136

AC:

703

AN:

5166

South Asian (SAS)

AF:

0.183

AC:

879

AN:

4800

European-Finnish (FIN)

AF:

0.225

AC:

2376

AN:

10558

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.248

AC:

16873

AN:

67962

Other (OTH)

AF:

0.249

AC:

524

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1519

3037

4556

6074

7593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.267

Hom.:

1024

Bravo

AF:

0.294

Asia WGS

AF:

0.168

AC:

584

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.3

(source)

DANN

Benign

0.55

PhyloP100

0.24

Splicing

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

Publications

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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