rs7860026

Positions:

• chr9-1500138-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 0.115 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;