rs13032621

Positions:

• chr2-235349706-G-A

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 0.0224 in 152,298 control chromosomes in the GnomAD database, including 47 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 0.022 (47 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0224 (3416/152298) while in subpopulation NFE AF= 0.0352 (2394/68030). AF 95% confidence interval is 0.034. There are 47 homozygotes in gnomad4. There are 1578 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3414 AN: 152180 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00613

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0224 AC: 3416 AN: 152298 Hom.: 47 Cov.: 33 AF XY: 0.0212 AC XY: 1578 AN XY: 74468

Gnomad4 AFR AF: 0.00611

Gnomad4 AMR AF: 0.0236

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0320 Hom.: 41

Bravo AF: 0.0226

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13032621; hg19: chr2-236258350;