rs2675899

Variant names:

• chr2-14565266-A-C
• rs2675899

Your query was ambiguous. Multiple possible variants found:

• chr2-14565266-A-C
• chr2-14565266-A-G

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 0.664 in 150,460 control chromosomes in the GnomAD database, including 34,439 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 0.66 (34439 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.664 AC: 99849 AN: 150344 Hom.: 34418 Cov.: 30

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.664 AC: 99922 AN: 150460 Hom.: 34439 Cov.: 30 AF XY: 0.662 AC XY: 48634 AN XY: 73482

African (AFR) AF: 0.593 AC: 24422 AN: 41214

American (AMR) AF: 0.619 AC: 9350 AN: 15102

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2613 AN: 3454

East Asian (EAS) AF: 0.764 AC: 3946 AN: 5162

South Asian (SAS) AF: 0.578 AC: 2751 AN: 4756

European-Finnish (FIN) AF: 0.671 AC: 6963 AN: 10378

Middle Eastern (MID) AF: 0.690 AC: 200 AN: 290

European-Non Finnish (NFE) AF: 0.709 AC: 47559 AN: 67108

Other (OTH) AF: 0.706 AC: 1476 AN: 2090

Alfa AF: 0.675 Hom.: 47355

Bravo AF: 0.662

Asia WGS AF: 0.676 AC: 2347 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.89
DANN	Benign	0.54
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs2675899; hg19: chr2-14705390;