10-103929831-C-T

Variant names:

• chr10-103929831-C-T
• rs1342214
• ENST00000698239.1:n.274-12175G>A

Variant summary

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

The ENST00000698239.1(ENSG00000289744):​n.274-12175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,878 control chromosomes in the GnomAD database, including 14,775 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 0.44 (14775 hom., cov: 31)
• Consequence: ENSG00000289744 ENST00000698239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 5 publications found

Genes affected

ENSG00000289744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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
ENSG00000289744	ENST00000698239.1	n.274-12175G>A		intron_variant	Intron 2 of 11
ENSG00000289744	ENST00000698240.1	n.389-12175G>A		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66115 AN: 151760 Hom.: 14749 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.436 AC: 66184 AN: 151878 Hom.: 14775 Cov.: 31 AF XY: 0.434 AC XY: 32204 AN XY: 74226

African (AFR) AF: 0.527 AC: 21784 AN: 41346

American (AMR) AF: 0.398 AC: 6080 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5174

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4814

European-Finnish (FIN) AF: 0.478 AC: 5037 AN: 10540

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27816 AN: 67966

Other (OTH) AF: 0.426 AC: 898 AN: 2108

Alfa AF: 0.389 Hom.: 5887

Bravo AF: 0.432

Asia WGS AF: 0.348 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1342214; hg19: chr10-105689589;