2-123504261-T-C

Variant names:

• chr2-123504261-T-C
• rs13022866

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 0.585 in 140,078 control chromosomes in the GnomAD database, including 23,230 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 0.59 (23230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.585 AC: 81926 AN: 139980 Hom.: 23213 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.524

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.585 AC: 81982 AN: 140078 Hom.: 23230 Cov.: 31 AF XY: 0.579 AC XY: 39477 AN XY: 68232

African (AFR) AF: 0.432 AC: 15284 AN: 35346

American (AMR) AF: 0.615 AC: 8762 AN: 14254

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1874 AN: 3312

East Asian (EAS) AF: 0.526 AC: 2310 AN: 4392

South Asian (SAS) AF: 0.525 AC: 2290 AN: 4366

European-Finnish (FIN) AF: 0.563 AC: 5464 AN: 9712

Middle Eastern (MID) AF: 0.537 AC: 145 AN: 270

European-Non Finnish (NFE) AF: 0.673 AC: 44161 AN: 65612

Other (OTH) AF: 0.596 AC: 1171 AN: 1966

Alfa AF: 0.615 Hom.: 6753

Bravo AF: 0.539

Asia WGS AF: 0.502 AC: 1727 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs13022866; hg19: chr2-124261837;