chr2-26005338-C-T

Position:

• chr2-26005338-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0342 in 151,960 control chromosomes in the GnomAD database, including 121 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 0.034 (121 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0342 (5202/151960) while in subpopulation NFE AF= 0.0489 (3319/67940). AF 95% confidence interval is 0.0475. There are 121 homozygotes in gnomad4. There are 2549 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 121 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5202 AN: 151842 Hom.: 121 Cov.: 31

Gnomad AFR AF: 0.00849

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0342 AC: 5202 AN: 151960 Hom.: 121 Cov.: 31 AF XY: 0.0343 AC XY: 2549 AN XY: 74268

Gnomad4 AFR AF: 0.00846

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.0432

Alfa AF: 0.0384 Hom.: 18

Bravo AF: 0.0320

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112288323; hg19: chr2-26228207;