chr5-160507870-T-C

Position:

• chr5-160507870-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.160507870T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;