rs7079770

Positions:

• chr10-32390904-C-G
• chr10-32390904-C-T

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 0.363 in 150,796 control chromosomes in the GnomAD database, including 10,469 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 0.36 (10469 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54620 AN: 150706 Hom.: 10443 Cov.: 29

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.363 AC: 54683 AN: 150796 Hom.: 10469 Cov.: 29 AF XY: 0.365 AC XY: 26809 AN XY: 73528

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.344

Alfa AF: 0.328 Hom.: 1016

Bravo AF: 0.369

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7079770; hg19: chr10-32679832;