10-92706670-T-C

Variant names:

• chr10-92706670-T-C
• rs11187139
• ENST00000788997.1:n.*72T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000788997.1(ENSG00000302698):​n.*72T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,814 control chromosomes in the GnomAD database, including 14,526 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 0.43 (14526 hom., cov: 31)
• Consequence: ENSG00000302698 ENST00000788997.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 8 publications found

Genes affected

ENSG00000302698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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
ENSG00000302698	ENST00000788997.1	n.*72T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64976 AN: 151698 Hom.: 14529 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.428 AC: 65007 AN: 151814 Hom.: 14526 Cov.: 31 AF XY: 0.433 AC XY: 32120 AN XY: 74162

African (AFR) AF: 0.374 AC: 15501 AN: 41408

American (AMR) AF: 0.468 AC: 7141 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3470

East Asian (EAS) AF: 0.824 AC: 4251 AN: 5158

South Asian (SAS) AF: 0.565 AC: 2714 AN: 4802

European-Finnish (FIN) AF: 0.473 AC: 4977 AN: 10514

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27716 AN: 67904

Other (OTH) AF: 0.419 AC: 879 AN: 2100

Alfa AF: 0.419 Hom.: 1693

Bravo AF: 0.429

Asia WGS AF: 0.621 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.60
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11187139; hg19: chr10-94466427;