rs10498496

Variant names:

• chr14-62467213-C-G
• rs10498496
• ENST00000743723.1:n.587-36831C>G

Variant summary

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

The ENST00000743723.1(ENSG00000296937):​n.587-36831C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,876 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: ENSG00000296937 ENST00000743723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370529	XR_943932.3	n.126-36828C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296937	ENST00000743723.1	n.587-36831C>G		intron_variant	Intron 2 of 4
ENSG00000296937	ENST00000743724.1	n.588-36831C>G		intron_variant	Intron 2 of 3
ENSG00000296937	ENST00000743725.1	n.333-36828C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19805 AN: 151758 Hom.: 1541 Cov.: 32

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.130 AC: 19816 AN: 151876 Hom.: 1537 Cov.: 32 AF XY: 0.133 AC XY: 9905 AN XY: 74216

African (AFR) AF: 0.0721 AC: 2990 AN: 41466

American (AMR) AF: 0.242 AC: 3680 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3470

East Asian (EAS) AF: 0.124 AC: 641 AN: 5166

South Asian (SAS) AF: 0.110 AC: 531 AN: 4826

European-Finnish (FIN) AF: 0.173 AC: 1825 AN: 10558

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9233 AN: 67850

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.125 Hom.: 171

Bravo AF: 0.136

Asia WGS AF: 0.111 AC: 385 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	5.7
DANN	Benign	0.41
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10498496; hg19: chr14-62933931;