rs7905482

Variant names:

• chr10-80104208-C-T
• rs7905482

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 0.342 in 151,970 control chromosomes in the GnomAD database, including 9,066 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 0.34 (9066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51870 AN: 151852 Hom.: 9062 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.342 AC: 51907 AN: 151970 Hom.: 9066 Cov.: 32 AF XY: 0.335 AC XY: 24867 AN XY: 74266

African (AFR) AF: 0.360 AC: 14926 AN: 41452

American (AMR) AF: 0.288 AC: 4394 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5166

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4798

European-Finnish (FIN) AF: 0.316 AC: 3340 AN: 10556

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24313 AN: 67950

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.345 Hom.: 28812

Bravo AF: 0.339

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.4
DANN	Benign	0.66
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7905482; hg19: chr10-81863964;