rs10486822

Variant names:

• chr7-81392646-T-A
• rs10486822

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.133 AC: 5540 AN: 41502

American (AMR) AF: 0.186 AC: 2837 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3464

East Asian (EAS) AF: 0.438 AC: 2257 AN: 5158

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1180 AN: 10578

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8959 AN: 67830

Other (OTH) AF: 0.151 AC: 318 AN: 2106

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
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs10486822; hg19: chr7-81021962;