rs7460090

Variant names:

• chr8-56281604-T-C
• rs7460090

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 0.139 in 150,198 control chromosomes in the GnomAD database, including 1,492 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 0.14 (1492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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: 0.139 AC: 20858 AN: 150108 Hom.: 1490 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.139 AC: 20869 AN: 150198 Hom.: 1492 Cov.: 32 AF XY: 0.138 AC XY: 10118 AN XY: 73436

African (AFR) AF: 0.192 AC: 7588 AN: 39616

American (AMR) AF: 0.140 AC: 2139 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3468

East Asian (EAS) AF: 0.0586 AC: 303 AN: 5174

South Asian (SAS) AF: 0.124 AC: 599 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10596

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.117 AC: 7949 AN: 67962

Other (OTH) AF: 0.155 AC: 326 AN: 2098

Alfa AF: 0.124 Hom.: 3787

Bravo AF: 0.141

Asia WGS AF: 0.118 AC: 410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.35
DANN	Benign	0.40
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7460090; hg19: chr8-57194163;