5-135964162-C-T

Variant names:

• chr5-135964162-C-T
• rs2526146

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 0.615 in 152,056 control chromosomes in the GnomAD database, including 28,977 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 0.62 (28977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 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: 0.615 AC: 93472 AN: 151938 Hom.: 28952 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.615 AC: 93534 AN: 152056 Hom.: 28977 Cov.: 32 AF XY: 0.616 AC XY: 45809 AN XY: 74332

African (AFR) AF: 0.573 AC: 23775 AN: 41466

American (AMR) AF: 0.659 AC: 10081 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3466

East Asian (EAS) AF: 0.628 AC: 3244 AN: 5168

South Asian (SAS) AF: 0.688 AC: 3317 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6575 AN: 10536

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42408 AN: 67990

Other (OTH) AF: 0.607 AC: 1279 AN: 2108

Alfa AF: 0.623 Hom.: 7199

Bravo AF: 0.613

Asia WGS AF: 0.666 AC: 2315 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	0.57
DANN	Benign	0.43
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2526146; hg19: chr5-135299851; COSMIC: COSV60200564;