rs26438

Variant names:

• chr5-165861916-C-T
• rs26438

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 0.483 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
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.483 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

African (AFR) AF: 0.545 AC: 22564 AN: 41378

American (AMR) AF: 0.554 AC: 8444 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3462

East Asian (EAS) AF: 0.707 AC: 3650 AN: 5162

South Asian (SAS) AF: 0.630 AC: 3036 AN: 4816

European-Finnish (FIN) AF: 0.522 AC: 5503 AN: 10538

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27544 AN: 67904

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.426 Hom.: 23877

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs26438; hg19: chr5-165288921;