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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307514	ENST00000826664.1		n.259-3028C>T		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.254-3033C>T		intron	N/A
	ENSG00000307514	ENST00000826667.1		n.312-3033C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10484035;

hg19: chr14-92778557;