rs7586898

Variant names:

• chr2-15821475-G-C
• rs7586898

Your query was ambiguous. Multiple possible variants found:

• chr2-15821475-G-C
• chr2-15821475-G-T

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 0.679 in 152,132 control chromosomes in the GnomAD database, including 38,079 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 0.68 (38079 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 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: 0.679 AC: 103211 AN: 152014 Hom.: 38070 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.679 AC: 103251 AN: 152132 Hom.: 38079 Cov.: 33 AF XY: 0.680 AC XY: 50592 AN XY: 74358

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.707

Alfa AF: 0.683 Hom.: 2422

Bravo AF: 0.653

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7586898; hg19: chr2-15961599;