5-157718184-T-C

Position:

• chr5-157718184-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 0.476 in 151,960 control chromosomes in the GnomAD database, including 17,565 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 0.48 (17565 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.157718184T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72197 AN: 151842 Hom.: 17530 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.476 AC: 72291 AN: 151960 Hom.: 17565 Cov.: 31 AF XY: 0.478 AC XY: 35493 AN XY: 74284

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.479

Alfa AF: 0.458 Hom.: 2731

Bravo AF: 0.469

Asia WGS AF: 0.476 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7731936; hg19: chr5-157145192;