4-167343098-C-T

Variant names:

• chr4-167343098-C-T
• rs13111850

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.949

Alfa AF: 0.958 Hom.: 110707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13111850; hg19: chr4-168264249;