4-141567731-C-T

Variant names:

• chr4-141567731-C-T
• rs7667746

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 0.741 in 151,710 control chromosomes in the GnomAD database, including 42,025 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 0.74 (42025 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.741 AC: 112378 AN: 151592 Hom.: 41976 Cov.: 29

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.741 AC: 112482 AN: 151710 Hom.: 42025 Cov.: 29 AF XY: 0.742 AC XY: 54932 AN XY: 74078

African (AFR) AF: 0.840 AC: 34772 AN: 41396

American (AMR) AF: 0.713 AC: 10859 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2488 AN: 3464

East Asian (EAS) AF: 0.840 AC: 4316 AN: 5138

South Asian (SAS) AF: 0.761 AC: 3644 AN: 4788

European-Finnish (FIN) AF: 0.696 AC: 7314 AN: 10502

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46754 AN: 67890

Other (OTH) AF: 0.710 AC: 1493 AN: 2102

Alfa AF: 0.715 Hom.: 8597

Bravo AF: 0.746

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.56
DANN	Benign	0.90
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7667746; hg19: chr4-142488884;