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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370529	XR_943932.3	n.126-10251A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296937	ENST00000743723.1	n.587-10254A>G		intron_variant	Intron 2 of 4
ENSG00000296937	ENST00000743724.1	n.588-10254A>G		intron_variant	Intron 2 of 3
ENSG00000296937	ENST00000743725.1	n.333-10251A>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs10498500; hg19: chr14-62960508;