rs4263608

Positions:

• chr6-157978417-G-A

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 0.158 in 151,968 control chromosomes in the GnomAD database, including 2,021 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 0.16 (2021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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 (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23944 AN: 151850 Hom.: 2018 Cov.: 31

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.158 AC: 23955 AN: 151968 Hom.: 2021 Cov.: 31 AF XY: 0.157 AC XY: 11661 AN XY: 74290

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.168

Alfa AF: 0.187 Hom.: 2862

Bravo AF: 0.156

Asia WGS AF: 0.150 AC: 519 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	0.16
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4263608; hg19: chr6-158399449;