rs10484035

Variant names:

• chr14-92312213-C-T
• rs10484035
• ENST00000826664.1:n.259-3028C>T

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.259-3028C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,878 control chromosomes in the GnomAD database, including 16,146 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 0.45 (16146 hom., cov: 31)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 2 publications found

Genes affected

ENSG00000307514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370627	XR_944153.1	n.132-3033C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307514	ENST00000826664.1	n.259-3028C>T		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826665.1	n.254-3033C>T		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826667.1	n.312-3033C>T		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826668.1	n.251-3028C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68271 AN: 151760 Hom.: 16109 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.450 AC: 68360 AN: 151878 Hom.: 16146 Cov.: 31 AF XY: 0.457 AC XY: 33948 AN XY: 74220

African (AFR) AF: 0.554 AC: 22917 AN: 41400

American (AMR) AF: 0.526 AC: 8033 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3026 AN: 5154

South Asian (SAS) AF: 0.558 AC: 2684 AN: 4806

European-Finnish (FIN) AF: 0.399 AC: 4199 AN: 10526

Middle Eastern (MID) AF: 0.538 AC: 156 AN: 290

European-Non Finnish (NFE) AF: 0.359 AC: 24356 AN: 67938

Other (OTH) AF: 0.482 AC: 1014 AN: 2102

Alfa AF: 0.421 Hom.: 3985

Bravo AF: 0.467

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10484035; hg19: chr14-92778557;