rs7679763

Variant names:

• chr4-179342790-T-C
• rs7679763

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 0.358 in 152,074 control chromosomes in the GnomAD database, including 10,406 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 0.36 (10406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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: 0.358 AC: 54427 AN: 151956 Hom.: 10385 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.358 AC: 54483 AN: 152074 Hom.: 10406 Cov.: 32 AF XY: 0.366 AC XY: 27175 AN XY: 74326

African (AFR) AF: 0.271 AC: 11245 AN: 41470

American (AMR) AF: 0.507 AC: 7743 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3040 AN: 5164

South Asian (SAS) AF: 0.472 AC: 2275 AN: 4824

European-Finnish (FIN) AF: 0.365 AC: 3849 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24004 AN: 67994

Other (OTH) AF: 0.343 AC: 724 AN: 2112

Alfa AF: 0.372 Hom.: 1376

Bravo AF: 0.363

Asia WGS AF: 0.500 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7679763; hg19: chr4-180263944;