rs112288323

Variant names:

• chr2-26005338-C-T
• rs112288323

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 121 gene

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: 0.0343 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

African (AFR) AF: 0.00846 AC: 351 AN: 41478

American (AMR) AF: 0.0371 AC: 566 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5168

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4820

European-Finnish (FIN) AF: 0.0465 AC: 490 AN: 10528

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0489 AC: 3319 AN: 67940

Other (OTH) AF: 0.0432 AC: 91 AN: 2108

Alfa AF: 0.0330 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
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs112288323; hg19: chr2-26228207;