rs1472268

Variant names:

• chr4-140571789-T-A
• rs1472268

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 152,050 control chromosomes in the GnomAD database, including 14,222 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 (14222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 59776 AN: 151932 Hom.: 14181 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.486

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: 59873 AN: 152050 Hom.: 14222 Cov.: 32 AF XY: 0.393 AC XY: 29180 AN XY: 74342

African (AFR) AF: 0.664 AC: 27520 AN: 41452

American (AMR) AF: 0.405 AC: 6172 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2512 AN: 5174

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

European-Finnish (FIN) AF: 0.217 AC: 2302 AN: 10588

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

European-Non Finnish (NFE) AF: 0.254 AC: 17245 AN: 67974

Other (OTH) AF: 0.357 AC: 751 AN: 2106

Alfa AF: 0.343 Hom.: 1341

Bravo AF: 0.419

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1472268; hg19: chr4-141492943;