rs7084667

Variant names:

• chr10-79988952-C-T
• rs7084667

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;