17-34687977-A-G

Variant names:

• chr17-34687977-A-G
• rs4795972

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 0.538 in 152,106 control chromosomes in the GnomAD database, including 22,567 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 0.54 (22567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.538 AC: 81755 AN: 151988 Hom.: 22553 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.538 AC: 81817 AN: 152106 Hom.: 22567 Cov.: 33 AF XY: 0.542 AC XY: 40317 AN XY: 74344

African (AFR) AF: 0.415 AC: 17210 AN: 41488

American (AMR) AF: 0.581 AC: 8893 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3127 AN: 5170

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4824

European-Finnish (FIN) AF: 0.695 AC: 7351 AN: 10574

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39287 AN: 67966

Other (OTH) AF: 0.539 AC: 1139 AN: 2112

Alfa AF: 0.564 Hom.: 13558

Bravo AF: 0.527

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4795972; hg19: chr17-33014996;