rs4629688

Positions:

• chr6-95659338-G-A
• chr6-95659338-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 0.854 in 152,024 control chromosomes in the GnomAD database, including 55,638 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 0.85 (55638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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: 0.854 AC: 129676 AN: 151906 Hom.: 55597 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.854 AC: 129772 AN: 152024 Hom.: 55638 Cov.: 32 AF XY: 0.852 AC XY: 63320 AN XY: 74304

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.879

Alfa AF: 0.829 Hom.: 8897

Bravo AF: 0.864

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4629688; hg19: chr6-96107214;