rs7905482

Variant names:

• chr10-80104208-C-T
• rs7905482

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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.342 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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.330

Alfa AF: 0.345 Hom.: 18854

Bravo AF: 0.339

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7905482; hg19: chr10-81863964;