17-7304878-C-T

Variant names:

• chr17-7304878-C-T
• rs4796398

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 0.556 in 151,834 control chromosomes in the GnomAD database, including 23,944 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 0.56 (23944 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 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: 0.555 AC: 84260 AN: 151718 Hom.: 23908 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.556 AC: 84352 AN: 151834 Hom.: 23944 Cov.: 31 AF XY: 0.564 AC XY: 41824 AN XY: 74204

African (AFR) AF: 0.455 AC: 18841 AN: 41376

American (AMR) AF: 0.608 AC: 9279 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3535 AN: 5178

South Asian (SAS) AF: 0.672 AC: 3241 AN: 4824

European-Finnish (FIN) AF: 0.694 AC: 7265 AN: 10474

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38765 AN: 67940

Other (OTH) AF: 0.540 AC: 1137 AN: 2106

Alfa AF: 0.558 Hom.: 86130

Bravo AF: 0.543

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.34
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4796398; hg19: chr17-7208197; COSMIC: COSV60554256;