rs2513858

Variant names:

• chr8-106813760-G-A
• rs2513858

Your query was ambiguous. Multiple possible variants found:

• chr8-106813760-G-A
• chr8-106813760-G-C
• chr8-106813760-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 0.705 in 152,146 control chromosomes in the GnomAD database, including 38,205 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 0.70 (38205 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.705 AC: 107136 AN: 152028 Hom.: 38164 Cov.: 33

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.705 AC: 107235 AN: 152146 Hom.: 38205 Cov.: 33 AF XY: 0.702 AC XY: 52208 AN XY: 74372

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.731

Alfa AF: 0.673 Hom.: 31820

Bravo AF: 0.719

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2513858; hg19: chr8-107825988;