rs2515192

Positions:

• chr8-103019945-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 0.581 in 152,098 control chromosomes in the GnomAD database, including 28,159 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 0.58 (28159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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 (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.581 AC: 88251 AN: 151980 Hom.: 28092 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.581 AC: 88373 AN: 152098 Hom.: 28159 Cov.: 32 AF XY: 0.574 AC XY: 42647 AN XY: 74330

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.522

Alfa AF: 0.536 Hom.: 8311

Bravo AF: 0.595

Asia WGS AF: 0.423 AC: 1475 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	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2515192; hg19: chr8-104032173;