rs7860026

Variant names:

• chr9-1500138-A-G
• rs7860026

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 0.115 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.142 AC: 5884 AN: 41478

American (AMR) AF: 0.0943 AC: 1442 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3464

East Asian (EAS) AF: 0.0559 AC: 289 AN: 5170

South Asian (SAS) AF: 0.0434 AC: 209 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7549 AN: 67978

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.107 Hom.: 730

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7860026; hg19: chr9-1500138;