chr17-7304878-C-T

Variant names:

• chr17-7304878-C-T
• rs4796398

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.540

Alfa AF: 0.555 Hom.: 31126

Bravo AF: 0.543

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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