chr17-56772968-A-G

Variant names:

• chr17-56772968-A-G
• rs4794665

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.488 in 152,036 control chromosomes in the GnomAD database, including 19,152 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 0.49 (19152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.488 AC: 74136 AN: 151918 Hom.: 19161 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.488 AC: 74147 AN: 152036 Hom.: 19152 Cov.: 32 AF XY: 0.495 AC XY: 36793 AN XY: 74308

African (AFR) AF: 0.334 AC: 13866 AN: 41484

American (AMR) AF: 0.661 AC: 10108 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1749 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4177 AN: 5178

South Asian (SAS) AF: 0.468 AC: 2251 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5509 AN: 10544

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34721 AN: 67952

Other (OTH) AF: 0.524 AC: 1104 AN: 2106

Alfa AF: 0.511 Hom.: 92477

Bravo AF: 0.499

Asia WGS AF: 0.624 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	19
DANN	Benign	0.73
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs4794665; hg19: chr17-54850329;