4-43535512-C-T

Variant names:

• chr4-43535512-C-T
• rs2347060

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 0.883 in 152,160 control chromosomes in the GnomAD database, including 59,579 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 0.88 (59579 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 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: 0.883 AC: 134258 AN: 152040 Hom.: 59533 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.883 AC: 134359 AN: 152160 Hom.: 59579 Cov.: 32 AF XY: 0.878 AC XY: 65318 AN XY: 74382

African (AFR) AF: 0.888 AC: 36877 AN: 41516

American (AMR) AF: 0.790 AC: 12058 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3034 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3612 AN: 5172

South Asian (SAS) AF: 0.778 AC: 3755 AN: 4824

European-Finnish (FIN) AF: 0.963 AC: 10218 AN: 10612

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61942 AN: 67976

Other (OTH) AF: 0.867 AC: 1834 AN: 2116

Alfa AF: 0.905 Hom.: 7587

Bravo AF: 0.868

Asia WGS AF: 0.736 AC: 2557 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2347060; hg19: chr4-43537529;