3-26839615-C-T

Variant names:

• chr3-26839615-C-T
• rs12635000

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 0.365 in 151,760 control chromosomes in the GnomAD database, including 10,962 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 0.37 (10962 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.366 AC: 55444 AN: 151640 Hom.: 10968 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.365 AC: 55468 AN: 151760 Hom.: 10962 Cov.: 31 AF XY: 0.369 AC XY: 27374 AN XY: 74170

African (AFR) AF: 0.249 AC: 10301 AN: 41392

American (AMR) AF: 0.449 AC: 6840 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3466

East Asian (EAS) AF: 0.638 AC: 3278 AN: 5140

South Asian (SAS) AF: 0.493 AC: 2379 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4132 AN: 10500

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26051 AN: 67890

Other (OTH) AF: 0.364 AC: 767 AN: 2110

Alfa AF: 0.382 Hom.: 46105

Bravo AF: 0.365

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.57
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12635000; hg19: chr3-26881106;