10-88794356-T-C

Variant names:

• chr10-88794356-T-C
• rs303502

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 0.796 in 152,116 control chromosomes in the GnomAD database, including 49,208 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 0.80 (49208 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 4 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 = 0.973 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: 0.796 AC: 120940 AN: 151998 Hom.: 49138 Cov.: 31

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.796 AC: 121070 AN: 152116 Hom.: 49208 Cov.: 31 AF XY: 0.800 AC XY: 59464 AN XY: 74338

African (AFR) AF: 0.945 AC: 39241 AN: 41544

American (AMR) AF: 0.809 AC: 12351 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2863 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5161 AN: 5182

South Asian (SAS) AF: 0.865 AC: 4171 AN: 4820

European-Finnish (FIN) AF: 0.725 AC: 7647 AN: 10548

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46882 AN: 67960

Other (OTH) AF: 0.802 AC: 1690 AN: 2108

Alfa AF: 0.732 Hom.: 22214

Bravo AF: 0.809

Asia WGS AF: 0.937 AC: 3255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.40
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs303502; hg19: chr10-90554113;