ENST00000849450.1:n.638+4102C>A

Variant names:

• chr10-113182606-C-A
• rs7915609
• ENST00000849450.1:n.638+4102C>A

Variant summary

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

The ENST00000849450.1(ENSG00000310382):​n.638+4102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,042 control chromosomes in the GnomAD database, including 16,100 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 0.40 (16100 hom., cov: 32)
• Consequence: ENSG00000310382 ENST00000849450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 3 publications found

Genes affected

ENSG00000310382 (HGNC:):

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 = 0.736 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
ENSG00000310382	ENST00000849450.1	n.638+4102C>A		intron_variant	Intron 3 of 3
ENSG00000310382	ENST00000849451.1	n.428+4102C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61017 AN: 151924 Hom.: 16049 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.402 AC: 61130 AN: 152042 Hom.: 16100 Cov.: 32 AF XY: 0.402 AC XY: 29871 AN XY: 74316

African (AFR) AF: 0.724 AC: 30019 AN: 41440

American (AMR) AF: 0.349 AC: 5329 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3909 AN: 5172

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2254 AN: 10558

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15362 AN: 67984

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.332 Hom.: 1936

Bravo AF: 0.425

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7915609; hg19: chr10-114942365;