rs4268090

Variant names:

• chr8-31623372-C-T
• rs4268090

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 0.352 in 151,910 control chromosomes in the GnomAD database, including 9,909 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 (9909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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: 0.352 AC: 53388 AN: 151792 Hom.: 9898 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.352 AC: 53410 AN: 151910 Hom.: 9909 Cov.: 32 AF XY: 0.355 AC XY: 26348 AN XY: 74206

African (AFR) AF: 0.247 AC: 10246 AN: 41464

American (AMR) AF: 0.330 AC: 5038 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3466

East Asian (EAS) AF: 0.557 AC: 2871 AN: 5154

South Asian (SAS) AF: 0.400 AC: 1928 AN: 4816

European-Finnish (FIN) AF: 0.427 AC: 4505 AN: 10548

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25938 AN: 67894

Other (OTH) AF: 0.393 AC: 829 AN: 2108

Alfa AF: 0.369 Hom.: 8252

Bravo AF: 0.339

Asia WGS AF: 0.434 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.83
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs4268090; hg19: chr8-31480888;