10-88794356-T-C

Position:

• chr10-88794356-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.88794356T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.802

Alfa AF: 0.734 Hom.: 20249

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs303502; hg19: chr10-90554113;