2-102259127-A-G

Variant names:

• chr2-102259127-A-G
• rs1345301

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 0.412 in 152,046 control chromosomes in the GnomAD database, including 14,451 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 0.41 (14451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.412 AC: 62620 AN: 151926 Hom.: 14466 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.412 AC: 62623 AN: 152046 Hom.: 14451 Cov.: 32 AF XY: 0.421 AC XY: 31282 AN XY: 74302

African (AFR) AF: 0.244 AC: 10108 AN: 41474

American (AMR) AF: 0.358 AC: 5465 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4346 AN: 5170

South Asian (SAS) AF: 0.653 AC: 3149 AN: 4826

European-Finnish (FIN) AF: 0.535 AC: 5636 AN: 10542

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31618 AN: 67966

Other (OTH) AF: 0.394 AC: 832 AN: 2110

Alfa AF: 0.432 Hom.: 1939

Bravo AF: 0.385

Asia WGS AF: 0.709 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1345301; hg19: chr2-102875587;