rs7669710

chr4-27371594-G-Achr4-27371594-G-Cchr4-27371594-G-T

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 0.384 in 151,994 control chromosomes in the GnomAD database, including 12,411 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 0.38 (12411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58277 AN: 151876 Hom.: 12403 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.384 AC: 58311 AN: 151994 Hom.: 12411 Cov.: 32 AF XY: 0.390 AC XY: 28964 AN XY: 74288

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.388

Alfa AF: 0.406 Hom.: 2260

Bravo AF: 0.379

Asia WGS AF: 0.615 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7669710; hg19: chr4-27373216;