5-119425846-C-T

Variant names:

• chr5-119425846-C-T
• rs2457221

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 0.462 in 151,932 control chromosomes in the GnomAD database, including 16,436 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 0.46 (16436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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: 0.462 AC: 70195 AN: 151814 Hom.: 16433 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.462 AC: 70227 AN: 151932 Hom.: 16436 Cov.: 32 AF XY: 0.461 AC XY: 34214 AN XY: 74280

African (AFR) AF: 0.450 AC: 18628 AN: 41416

American (AMR) AF: 0.438 AC: 6689 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1428 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5154

South Asian (SAS) AF: 0.542 AC: 2615 AN: 4822

European-Finnish (FIN) AF: 0.414 AC: 4362 AN: 10544

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32614 AN: 67924

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.464 Hom.: 3322

Bravo AF: 0.457

Asia WGS AF: 0.489 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.37
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2457221; hg19: chr5-118761541;