rs1265138

Variant names:

• chr8-102187808-A-G
• rs1265138

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.115 AC: 4790 AN: 41548

American (AMR) AF: 0.0805 AC: 1232 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1684 AN: 5182

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4822

European-Finnish (FIN) AF: 0.0102 AC: 108 AN: 10628

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2382 AN: 68018

Other (OTH) AF: 0.0766 AC: 162 AN: 2116

Alfa AF: 0.0581 Hom.: 1437

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
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1265138; hg19: chr8-103200036;