chr10-78821014-A-G

Variant names:

• chr10-78821014-A-G
• rs10762810

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 0.293 in 152,208 control chromosomes in the GnomAD database, including 7,216 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 0.29 (7216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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: 0.293 AC: 44632 AN: 152090 Hom.: 7214 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44651 AN: 152208 Hom.: 7216 Cov.: 32 AF XY: 0.294 AC XY: 21846 AN XY: 74418

African (AFR) AF: 0.158 AC: 6544 AN: 41546

American (AMR) AF: 0.299 AC: 4575 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1721 AN: 5182

South Asian (SAS) AF: 0.405 AC: 1955 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24467 AN: 67986

Other (OTH) AF: 0.300 AC: 634 AN: 2114

Alfa AF: 0.353 Hom.: 7959

Bravo AF: 0.282

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.82
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10762810; hg19: chr10-80580771;