rs7586898

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;