rs7860026

Variant names:

• chr9-1500138-A-G
• rs7860026

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 0.115 in 152,100 control chromosomes in the GnomAD database, including 1,050 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 0.11 (1050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

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 = 0.139 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: 0.115 AC: 17446 AN: 151982 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17447 AN: 152100 Hom.: 1050 Cov.: 32 AF XY: 0.113 AC XY: 8370 AN XY: 74340

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0559

Gnomad4 SAS AF: 0.0434

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.119

Alfa AF: 0.106 Hom.: 601

Bravo AF: 0.116

Asia WGS AF: 0.0480 AC: 169 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	3.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7860026; hg19: chr9-1500138;