rs4263608

Variant names:

• chr6-157978417-G-A
• rs4263608

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 0.158 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0925 AC: 3831 AN: 41424

American (AMR) AF: 0.159 AC: 2424 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3464

East Asian (EAS) AF: 0.123 AC: 635 AN: 5166

South Asian (SAS) AF: 0.187 AC: 898 AN: 4794

European-Finnish (FIN) AF: 0.161 AC: 1700 AN: 10562

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13332 AN: 67966

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.175 Hom.: 3960

Bravo AF: 0.156

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.79
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4263608; hg19: chr6-158399449;