rs1076392

Variant names:

• chr17-61415647-T-C
• rs1076392

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 0.61 in 152,102 control chromosomes in the GnomAD database, including 28,947 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 0.61 (28947 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.610 AC: 92640 AN: 151982 Hom.: 28922 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.610 AC: 92707 AN: 152102 Hom.: 28947 Cov.: 33 AF XY: 0.616 AC XY: 45771 AN XY: 74352

African (AFR) AF: 0.467 AC: 19347 AN: 41468

American (AMR) AF: 0.617 AC: 9438 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2441 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3361 AN: 5162

South Asian (SAS) AF: 0.611 AC: 2944 AN: 4822

European-Finnish (FIN) AF: 0.736 AC: 7796 AN: 10592

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.666 AC: 45276 AN: 67986

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.581 Hom.: 7067

Bravo AF: 0.595

Asia WGS AF: 0.594 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1076392; hg19: chr17-59493008;