rs10499882

Positions:

• chr7-84875329-T-C

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 0.234 in 152,072 control chromosomes in the GnomAD database, including 4,998 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 0.23 (4998 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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: 0.234 AC: 35517 AN: 151954 Hom.: 4984 Cov.: 31

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.234 AC: 35541 AN: 152072 Hom.: 4998 Cov.: 31 AF XY: 0.235 AC XY: 17446 AN XY: 74312

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.274

Alfa AF: 0.278 Hom.: 6172

Bravo AF: 0.237

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499882; hg19: chr7-84504645;