chr4-159506641-C-T

Variant names:

• chr4-159506641-C-T
• rs1317266

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 0.798 in 152,070 control chromosomes in the GnomAD database, including 48,445 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 0.80 (48445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.798 AC: 121189 AN: 151950 Hom.: 48408 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.798 AC: 121278 AN: 152070 Hom.: 48445 Cov.: 31 AF XY: 0.800 AC XY: 59439 AN XY: 74342

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.788

Alfa AF: 0.782 Hom.: 21180

Bravo AF: 0.804

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317266; hg19: chr4-160427793;