chr2-232423842-T-A

Variant names:

• chr2-232423842-T-A
• rs13016319

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 0.19 in 150,984 control chromosomes in the GnomAD database, including 3,543 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 0.19 (3543 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.190 AC: 28666 AN: 150866 Hom.: 3540 Cov.: 31

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.190 AC: 28658 AN: 150984 Hom.: 3543 Cov.: 31 AF XY: 0.188 AC XY: 13924 AN XY: 73896

African (AFR) AF: 0.0489 AC: 1980 AN: 40480

American (AMR) AF: 0.183 AC: 2778 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3468

East Asian (EAS) AF: 0.0406 AC: 210 AN: 5170

South Asian (SAS) AF: 0.177 AC: 854 AN: 4812

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10578

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18137 AN: 67960

Other (OTH) AF: 0.215 AC: 452 AN: 2098

Alfa AF: 0.214 Hom.: 481

Bravo AF: 0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.38
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs13016319; hg19: chr2-233288552;