rs1265138

Positions:

• chr8-102187808-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 0.0775 in 152,286 control chromosomes in the GnomAD database, including 836 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 0.077 (836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11786 AN: 152168 Hom.: 832 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0775 AC: 11797 AN: 152286 Hom.: 836 Cov.: 32 AF XY: 0.0800 AC XY: 5955 AN XY: 74482

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.0972

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0510 Hom.: 403

Bravo AF: 0.0843

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.8
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265138; hg19: chr8-103200036;