rs4628236

Variant names:

• chr8-109159916-G-A
• rs4628236

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 0.347 in 151,936 control chromosomes in the GnomAD database, including 9,513 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 0.35 (9513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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: 0.347 AC: 52730 AN: 151818 Hom.: 9504 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.347 AC: 52777 AN: 151936 Hom.: 9513 Cov.: 32 AF XY: 0.352 AC XY: 26118 AN XY: 74234

African (AFR) AF: 0.293 AC: 12161 AN: 41436

American (AMR) AF: 0.440 AC: 6709 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2435 AN: 5166

South Asian (SAS) AF: 0.429 AC: 2065 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4146 AN: 10534

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23301 AN: 67944

Other (OTH) AF: 0.333 AC: 703 AN: 2114

Alfa AF: 0.350 Hom.: 1910

Bravo AF: 0.348

Asia WGS AF: 0.476 AC: 1656 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	2.4
DANN	Benign	0.70
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4628236; hg19: chr8-110172145;