4-156990873-C-T

Variant names:

• chr4-156990873-C-T
• rs7674099

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 0.815 in 152,172 control chromosomes in the GnomAD database, including 50,895 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 0.81 (50895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.856 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: 0.815 AC: 123880 AN: 152056 Hom.: 50857 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.815 AC: 123970 AN: 152172 Hom.: 50895 Cov.: 32 AF XY: 0.813 AC XY: 60480 AN XY: 74386

African (AFR) AF: 0.732 AC: 30395 AN: 41516

American (AMR) AF: 0.866 AC: 13240 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2916 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3429 AN: 5146

South Asian (SAS) AF: 0.747 AC: 3605 AN: 4828

European-Finnish (FIN) AF: 0.862 AC: 9131 AN: 10596

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58578 AN: 68006

Other (OTH) AF: 0.836 AC: 1765 AN: 2112

Alfa AF: 0.847 Hom.: 40003

Bravo AF: 0.811

Asia WGS AF: 0.744 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs7674099; hg19: chr4-157912025;