chr5-165861916-C-T

Position:

• chr5-165861916-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 0.483 in 151,806 control chromosomes in the GnomAD database, including 18,453 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 (18453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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 = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73280 AN: 151688 Hom.: 18416 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.483 AC: 73366 AN: 151806 Hom.: 18453 Cov.: 32 AF XY: 0.493 AC XY: 36555 AN XY: 74170

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.455

Alfa AF: 0.420 Hom.: 18466

Bravo AF: 0.485

Asia WGS AF: 0.652 AC: 2265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26438; hg19: chr5-165288921;