17-56762398-C-A

Variant names:

• chr17-56762398-C-A
• rs1401796

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 0.547 in 152,010 control chromosomes in the GnomAD database, including 23,323 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 0.55 (23323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83050 AN: 151892 Hom.: 23318 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.547 AC: 83096 AN: 152010 Hom.: 23323 Cov.: 32 AF XY: 0.554 AC XY: 41114 AN XY: 74274

African (AFR) AF: 0.505 AC: 20905 AN: 41426

American (AMR) AF: 0.684 AC: 10457 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4641 AN: 5160

South Asian (SAS) AF: 0.503 AC: 2424 AN: 4816

European-Finnish (FIN) AF: 0.546 AC: 5764 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35261 AN: 67976

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.538 Hom.: 37287

Bravo AF: 0.561

Asia WGS AF: 0.687 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0080
DANN	Benign	0.35
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1401796; hg19: chr17-54839759;