rs17513961

Variant names:

• chr7-46352969-T-G
• rs17513961

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 0.0701 in 152,056 control chromosomes in the GnomAD database, including 540 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 0.070 (540 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0702 AC: 10669 AN: 151938 Hom.: 540 Cov.: 31

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0837

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0701 AC: 10665 AN: 152056 Hom.: 540 Cov.: 31 AF XY: 0.0692 AC XY: 5142 AN XY: 74334

African (AFR) AF: 0.0159 AC: 662 AN: 41518

American (AMR) AF: 0.0501 AC: 765 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4814

European-Finnish (FIN) AF: 0.112 AC: 1177 AN: 10542

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7158 AN: 67956

Other (OTH) AF: 0.0679 AC: 143 AN: 2106

Alfa AF: 0.0874 Hom.: 1637

Bravo AF: 0.0624

Asia WGS AF: 0.0140 AC: 50 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs17513961; hg19: chr7-46392567;