chr5-157899441-T-C

Position:

• chr5-157899441-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 0.117 in 152,220 control chromosomes in the GnomAD database, including 1,210 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 0.12 (1210 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17868 AN: 152102 Hom.: 1211 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.117 AC: 17884 AN: 152220 Hom.: 1210 Cov.: 33 AF XY: 0.119 AC XY: 8872 AN XY: 74422

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0908 Hom.: 145

Bravo AF: 0.116

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2448412; hg19: chr5-157326449;