rs10822492

Variant names:

• chr10-65322172-C-T
• rs10822492

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 0.28 in 151,656 control chromosomes in the GnomAD database, including 6,578 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 0.28 (6578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 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: 0.281 AC: 42509 AN: 151540 Hom.: 6576 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.280 AC: 42513 AN: 151656 Hom.: 6578 Cov.: 32 AF XY: 0.285 AC XY: 21134 AN XY: 74056

African (AFR) AF: 0.168 AC: 6960 AN: 41384

American (AMR) AF: 0.228 AC: 3474 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2909 AN: 5122

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3879 AN: 10498

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21407 AN: 67842

Other (OTH) AF: 0.276 AC: 580 AN: 2104

Alfa AF: 0.274 Hom.: 1059

Bravo AF: 0.269

Asia WGS AF: 0.442 AC: 1532 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10822492; hg19: chr10-67081930;