5-160507870-T-C

Variant names:

• chr5-160507870-T-C
• rs4921144

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 0.71 in 152,058 control chromosomes in the GnomAD database, including 39,856 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 0.71 (39856 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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: 0.710 AC: 107862 AN: 151940 Hom.: 39791 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.710 AC: 107993 AN: 152058 Hom.: 39856 Cov.: 31 AF XY: 0.712 AC XY: 52920 AN XY: 74328

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.710

Alfa AF: 0.661 Hom.: 8533

Bravo AF: 0.735

Asia WGS AF: 0.889 AC: 3087 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4921144; hg19: chr5-159934877;