17-12291963-T-A

Variant names:

• chr17-12291963-T-A
• rs1558103

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 0.914 in 152,226 control chromosomes in the GnomAD database, including 64,748 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 0.91 (64748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139109 AN: 152110 Hom.: 64729 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.914 AC: 139177 AN: 152226 Hom.: 64748 Cov.: 32 AF XY: 0.917 AC XY: 68227 AN XY: 74432

African (AFR) AF: 0.718 AC: 29788 AN: 41482

American (AMR) AF: 0.957 AC: 14644 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3374 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5157 AN: 5168

South Asian (SAS) AF: 0.996 AC: 4805 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10618

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67649 AN: 68042

Other (OTH) AF: 0.927 AC: 1955 AN: 2108

Alfa AF: 0.948 Hom.: 8588

Bravo AF: 0.902

Asia WGS AF: 0.966 AC: 3361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1558103; hg19: chr17-12195280;