10-92703125-C-T

Variant names:

• chr10-92703125-C-T
• rs1111875
• ENST00000788997.1:n.151+3010C>T

Variant summary

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

The ENST00000788997.1(ENSG00000302698):​n.151+3010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,048 control chromosomes in the GnomAD database, including 11,515 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 0.37 (11515 hom., cov: 32)
• Consequence: ENSG00000302698 ENST00000788997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 429 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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.151+3010C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56465 AN: 151930 Hom.: 11518 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.371 AC: 56481 AN: 152048 Hom.: 11515 Cov.: 32 AF XY: 0.377 AC XY: 28014 AN XY: 74344

African (AFR) AF: 0.229 AC: 9483 AN: 41446

American (AMR) AF: 0.334 AC: 5105 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3725 AN: 5186

South Asian (SAS) AF: 0.572 AC: 2764 AN: 4830

European-Finnish (FIN) AF: 0.475 AC: 5020 AN: 10572

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27789 AN: 67960

Other (OTH) AF: 0.366 AC: 773 AN: 2110

Alfa AF: 0.385 Hom.: 13730

Bravo AF: 0.354

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.64
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs1111875; hg19: chr10-94462882;