4-140569265-T-G

Variant names:

• chr4-140569265-T-G
• rs3811787

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 0.376 in 152,162 control chromosomes in the GnomAD database, including 12,669 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 0.38 (12669 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.375 AC: 57066 AN: 152044 Hom.: 12645 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.376 AC: 57140 AN: 152162 Hom.: 12669 Cov.: 33 AF XY: 0.378 AC XY: 28132 AN XY: 74372

African (AFR) AF: 0.610 AC: 25313 AN: 41530

American (AMR) AF: 0.374 AC: 5722 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2605 AN: 5134

South Asian (SAS) AF: 0.406 AC: 1962 AN: 4830

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10598

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16731 AN: 67982

Other (OTH) AF: 0.354 AC: 750 AN: 2116

Alfa AF: 0.293 Hom.: 5685

Bravo AF: 0.394

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-2.7
PromoterAI		-0.049	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3811787; hg19: chr4-141490419;