rs10498464

Variant names:

• chr14-53904864-G-A
• rs10498464
• ENST00000729148.1:n.495+10403C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-53904864-G-A
• chr14-53904864-G-T

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.495+10403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,742 control chromosomes in the GnomAD database, including 4,312 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 0.23 (4312 hom., cov: 33)
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 6 publications found

Genes affected

ENSG00000295303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984676	XR_001750978.2	n.308+10403C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295303	ENST00000729148.1	n.495+10403C>T		intron_variant	Intron 3 of 4
ENSG00000295303	ENST00000729149.1	n.448+10403C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34673 AN: 151624 Hom.: 4298 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.229 AC: 34718 AN: 151742 Hom.: 4312 Cov.: 33 AF XY: 0.236 AC XY: 17465 AN XY: 74104

African (AFR) AF: 0.188 AC: 7769 AN: 41340

American (AMR) AF: 0.342 AC: 5213 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2232 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1595 AN: 4806

European-Finnish (FIN) AF: 0.223 AC: 2337 AN: 10482

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13866 AN: 67928

Other (OTH) AF: 0.255 AC: 537 AN: 2106

Alfa AF: 0.213 Hom.: 2924

Bravo AF: 0.234

Asia WGS AF: 0.357 AC: 1234 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.65
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10498464; hg19: chr14-54371582;