rs10499881

Variant names:

• chr7-84613069-G-A
• rs10499881

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 0.0135 in 152,108 control chromosomes in the GnomAD database, including 98 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 0.013 (98 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 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: 0.0135 AC: 2057 AN: 151990 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.00991

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00412

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0135 AC: 2053 AN: 152108 Hom.: 98 Cov.: 32 AF XY: 0.0150 AC XY: 1115 AN XY: 74356

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.00991

Gnomad4 NFE AF: 0.00412

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00858 Hom.: 4

Bravo AF: 0.0168

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
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: rs10499881; hg19: chr7-84242385; COSMIC: COSV70094443;