rs1345302

Variant names:

• chr2-102256909-A-G
• rs1345302

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 152,042 control chromosomes in the GnomAD database, including 14,457 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 (14457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 62587 AN: 151920 Hom.: 14472 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.351

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: 62588 AN: 152042 Hom.: 14457 Cov.: 32 AF XY: 0.421 AC XY: 31253 AN XY: 74312

African (AFR) AF: 0.243 AC: 10090 AN: 41494

American (AMR) AF: 0.357 AC: 5452 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1018 AN: 3466

East Asian (EAS) AF: 0.841 AC: 4344 AN: 5164

South Asian (SAS) AF: 0.655 AC: 3163 AN: 4826

European-Finnish (FIN) AF: 0.535 AC: 5633 AN: 10532

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31607 AN: 67964

Other (OTH) AF: 0.394 AC: 833 AN: 2112

Alfa AF: 0.431 Hom.: 1937

Bravo AF: 0.385

Asia WGS AF: 0.709 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.62
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1345302; hg19: chr2-102873369;