rs10486822

Variant names:

• chr7-81392646-T-A
• rs10486822

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 0.155 in 151,934 control chromosomes in the GnomAD database, including 2,109 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 0.15 (2109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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: 0.155 AC: 23457 AN: 151816 Hom.: 2106 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23480 AN: 151934 Hom.: 2109 Cov.: 32 AF XY: 0.157 AC XY: 11677 AN XY: 74256

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.151

Alfa AF: 0.140 Hom.: 196

Bravo AF: 0.159

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486822; hg19: chr7-81021962;