5-112458257-C-T

Variant names:

• chr5-112458257-C-T
• rs163622

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0462 in 151,994 control chromosomes in the GnomAD database, including 212 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 0.046 (212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0627 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: 0.0462 AC: 7013 AN: 151876 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0165

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0462 AC: 7015 AN: 151994 Hom.: 212 Cov.: 32 AF XY: 0.0462 AC XY: 3436 AN XY: 74292

African (AFR) AF: 0.0175 AC: 728 AN: 41508

American (AMR) AF: 0.0443 AC: 675 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0165 AC: 57 AN: 3464

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0405 AC: 195 AN: 4814

European-Finnish (FIN) AF: 0.0751 AC: 790 AN: 10524

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4372 AN: 67958

Other (OTH) AF: 0.0460 AC: 97 AN: 2108

Alfa AF: 0.0506 Hom.: 33

Bravo AF: 0.0420

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs163622; hg19: chr5-111793954;