rs7084793

Variant names:

• chr10-45369631-T-C
• rs7084793

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 0.168 in 152,086 control chromosomes in the GnomAD database, including 2,201 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 0.17 (2201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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: 0.168 AC: 25458 AN: 151968 Hom.: 2194 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.168 AC: 25495 AN: 152086 Hom.: 2201 Cov.: 32 AF XY: 0.169 AC XY: 12569 AN XY: 74346

African (AFR) AF: 0.176 AC: 7296 AN: 41506

American (AMR) AF: 0.134 AC: 2046 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3466

East Asian (EAS) AF: 0.183 AC: 947 AN: 5176

South Asian (SAS) AF: 0.191 AC: 922 AN: 4822

European-Finnish (FIN) AF: 0.194 AC: 2056 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11056 AN: 67932

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.160 Hom.: 282

Bravo AF: 0.163

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.20
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7084793; hg19: chr10-45865079;