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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.706

Alfa AF: 0.690 Hom.: 21401

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675899; hg19: chr2-14705390;