4-188940097-G-T

Variant names:

• chr4-188940097-G-T
• rs11731175

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 0.334 in 151,922 control chromosomes in the GnomAD database, including 9,502 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 0.33 (9502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.334 AC: 50702 AN: 151804 Hom.: 9495 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.334 AC: 50739 AN: 151922 Hom.: 9502 Cov.: 32 AF XY: 0.338 AC XY: 25112 AN XY: 74234

African (AFR) AF: 0.319 AC: 13203 AN: 41440

American (AMR) AF: 0.421 AC: 6432 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3466

East Asian (EAS) AF: 0.828 AC: 4267 AN: 5154

South Asian (SAS) AF: 0.400 AC: 1920 AN: 4806

European-Finnish (FIN) AF: 0.351 AC: 3693 AN: 10536

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19550 AN: 67940

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.322 Hom.: 7560

Bravo AF: 0.343

Asia WGS AF: 0.599 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11731175; hg19: chr4-189861251;