15-60317231-C-T

Variant names:

• chr15-60317231-C-T
• rs11853426

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.442 in 151,758 control chromosomes in the GnomAD database, including 14,962 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 0.44 (14962 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67096 AN: 151640 Hom.: 14948 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.442

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.442 AC: 67145 AN: 151758 Hom.: 14962 Cov.: 30 AF XY: 0.444 AC XY: 32930 AN XY: 74118

African (AFR) AF: 0.406 AC: 16808 AN: 41402

American (AMR) AF: 0.564 AC: 8591 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.520 AC: 2672 AN: 5142

South Asian (SAS) AF: 0.419 AC: 2004 AN: 4780

European-Finnish (FIN) AF: 0.443 AC: 4651 AN: 10504

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29326 AN: 67922

Other (OTH) AF: 0.441 AC: 929 AN: 2106

Alfa AF: 0.422 Hom.: 2553

Bravo AF: 0.454

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.31
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs11853426; hg19: chr15-60609430;