rs10498500

Variant names:

• chr14-62493790-A-G
• rs10498500
• ENST00000743723.1:n.587-10254A>G

Variant summary

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

The ENST00000743723.1(ENSG00000296937):​n.587-10254A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,176 control chromosomes in the GnomAD database, including 2,228 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 0.15 (2228 hom., cov: 32)
• Consequence: ENSG00000296937 ENST00000743723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 1 publications found

Genes affected

ENSG00000296937 (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 (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743723.1. 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
	ENSG00000296937	ENST00000743723.1		n.587-10254A>G		intron	N/A
	ENSG00000296937	ENST00000743724.1		n.588-10254A>G		intron	N/A
	ENSG00000296937	ENST00000743725.1		n.333-10251A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22808 AN: 152058 Hom.: 2213 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.150 AC: 22864 AN: 152176 Hom.: 2228 Cov.: 32 AF XY: 0.145 AC XY: 10794 AN XY: 74398

African (AFR) AF: 0.271 AC: 11229 AN: 41508

American (AMR) AF: 0.101 AC: 1536 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3466

East Asian (EAS) AF: 0.0212 AC: 110 AN: 5182

South Asian (SAS) AF: 0.110 AC: 533 AN: 4828

European-Finnish (FIN) AF: 0.0602 AC: 638 AN: 10592

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8035 AN: 67998

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.138 Hom.: 360

Bravo AF: 0.158

Asia WGS AF: 0.101 AC: 351 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	2.5
DANN	Benign	0.24
PhyloP100		0.13

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: rs10498500;

hg19: chr14-62960508;