14-53904864-G-A

Variant names:

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729148.1. 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
	ENSG00000295303	ENST00000729148.1		n.495+10403C>T		intron	N/A
	ENSG00000295303	ENST00000729149.1		n.448+10403C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10498464;

hg19: chr14-54371582;