rs10487245

Variant names:

• chr7-94084209-G-A
• rs10487245

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 0.0851 in 152,210 control chromosomes in the GnomAD database, including 787 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 0.085 (787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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 = 0.15 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: 0.0849 AC: 12913 AN: 152092 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0851 AC: 12949 AN: 152210 Hom.: 787 Cov.: 32 AF XY: 0.0854 AC XY: 6353 AN XY: 74416

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0421

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0753 Hom.: 199

Bravo AF: 0.0950

Asia WGS AF: 0.127 AC: 444 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	15
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487245; hg19: chr7-93713521;