4-140571850-A-G

Variant names:

• chr4-140571850-A-G
• rs1472269

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 0.394 in 152,070 control chromosomes in the GnomAD database, including 14,226 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 0.39 (14226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.393 AC: 59789 AN: 151952 Hom.: 14185 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.394 AC: 59886 AN: 152070 Hom.: 14226 Cov.: 32 AF XY: 0.392 AC XY: 29179 AN XY: 74350

African (AFR) AF: 0.664 AC: 27515 AN: 41464

American (AMR) AF: 0.405 AC: 6181 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2518 AN: 5178

South Asian (SAS) AF: 0.372 AC: 1796 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10578

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17257 AN: 67984

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.338 Hom.: 1698

Bravo AF: 0.420

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1472269; hg19: chr4-141493004;