5-71950137-C-T

Variant names:

• chr5-71950137-C-T
• rs1217745

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 0.183 in 152,150 control chromosomes in the GnomAD database, including 2,718 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 0.18 (2718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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: 0.183 AC: 27846 AN: 152032 Hom.: 2714 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 27876 AN: 152150 Hom.: 2718 Cov.: 32 AF XY: 0.187 AC XY: 13901 AN XY: 74386

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.190

Alfa AF: 0.162 Hom.: 2517

Bravo AF: 0.187

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1217745; hg19: chr5-71245964;