rs7084667

Positions:

• chr10-79988952-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 0.295 in 152,046 control chromosomes in the GnomAD database, including 7,082 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 0.30 (7082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 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: 0.295 AC: 44830 AN: 151928 Hom.: 7076 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44854 AN: 152046 Hom.: 7082 Cov.: 32 AF XY: 0.294 AC XY: 21832 AN XY: 74302

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.282

Alfa AF: 0.318 Hom.: 15658

Bravo AF: 0.277

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7084667; hg19: chr10-81748708;