rs10498280

Variant names:

• chr14-25276981-A-C
• rs10498280
• ENST00000837960.1:n.380-2042A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-25276981-A-C
• chr14-25276981-A-T

Variant summary

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

The ENST00000837960.1(ENSG00000309034):​n.380-2042A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,050 control chromosomes in the GnomAD database, including 16,484 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 0.47 (16484 hom., cov: 33)
• Consequence: ENSG00000309034 ENST00000837960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 2 publications found

Genes affected

ENSG00000309034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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
ENSG00000309034	ENST00000837960.1	n.380-2042A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70683 AN: 151932 Hom.: 16456 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.465 AC: 70754 AN: 152050 Hom.: 16484 Cov.: 33 AF XY: 0.468 AC XY: 34740 AN XY: 74298

African (AFR) AF: 0.449 AC: 18613 AN: 41438

American (AMR) AF: 0.464 AC: 7087 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2571 AN: 5172

South Asian (SAS) AF: 0.484 AC: 2335 AN: 4822

European-Finnish (FIN) AF: 0.491 AC: 5185 AN: 10568

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32060 AN: 67984

Other (OTH) AF: 0.470 AC: 994 AN: 2116

Alfa AF: 0.301 Hom.: 688

Bravo AF: 0.462

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10498280; hg19: chr14-25746187;