4-167343098-C-T

Variant names:

• chr4-167343098-C-T
• rs13111850

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 0.965 in 152,114 control chromosomes in the GnomAD database, including 70,857 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 0.96 (70857 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 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: 0.965 AC: 146653 AN: 151996 Hom.: 70796 Cov.: 30

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.965 AC: 146772 AN: 152114 Hom.: 70857 Cov.: 30 AF XY: 0.965 AC XY: 71713 AN XY: 74342

African (AFR) AF: 0.991 AC: 41077 AN: 41454

American (AMR) AF: 0.913 AC: 13960 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3472

East Asian (EAS) AF: 0.969 AC: 4982 AN: 5144

South Asian (SAS) AF: 0.974 AC: 4701 AN: 4826

European-Finnish (FIN) AF: 0.988 AC: 10467 AN: 10598

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65112 AN: 68018

Other (OTH) AF: 0.949 AC: 2002 AN: 2110

Alfa AF: 0.960 Hom.: 253354

Bravo AF: 0.960

Asia WGS AF: 0.976 AC: 3393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.24
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs13111850; hg19: chr4-168264249;