5-111166731-C-T

Position:

• chr5-111166731-C-T

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 0.0878 in 152,156 control chromosomes in the GnomAD database, including 879 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 0.088 (879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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 = 0.193 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: 0.0878 AC: 13345 AN: 152038 Hom.: 879 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0878 AC: 13355 AN: 152156 Hom.: 879 Cov.: 32 AF XY: 0.0879 AC XY: 6538 AN XY: 74380

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0741

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0651 Hom.: 66

Bravo AF: 0.0922

Asia WGS AF: 0.154 AC: 536 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	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17132883; hg19: chr5-110502429;