chr10-88793294-A-G

Variant names:

• chr10-88793294-A-G
• rs303499

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 0.705 in 152,130 control chromosomes in the GnomAD database, including 38,510 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 0.71 (38510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• 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 (AFR) allele frequency at 95% confidence interval = 0.851 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: 0.705 AC: 107146 AN: 152012 Hom.: 38460 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.705 AC: 107258 AN: 152130 Hom.: 38510 Cov.: 33 AF XY: 0.703 AC XY: 52276 AN XY: 74366

African (AFR) AF: 0.858 AC: 35640 AN: 41526

American (AMR) AF: 0.689 AC: 10521 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3600 AN: 5170

South Asian (SAS) AF: 0.645 AC: 3111 AN: 4824

European-Finnish (FIN) AF: 0.641 AC: 6772 AN: 10572

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43133 AN: 67972

Other (OTH) AF: 0.707 AC: 1495 AN: 2116

Alfa AF: 0.652 Hom.: 114147

Bravo AF: 0.720

Asia WGS AF: 0.674 AC: 2341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs303499; hg19: chr10-90553051;