rs10484713

Variant names:

• chr6-140299747-C-T
• rs10484713
• ENST00000683950.1:n.202-15083C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000683950.1(ENSG00000288714):​n.202-15083C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,956 control chromosomes in the GnomAD database, including 2,983 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 0.17 (2983 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288714	ENST00000683950.1	n.202-15083C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26003 AN: 151838 Hom.: 2982 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.171 AC: 25996 AN: 151956 Hom.: 2983 Cov.: 32 AF XY: 0.168 AC XY: 12509 AN XY: 74258

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.176

Alfa AF: 0.212 Hom.: 501

Bravo AF: 0.155

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484713; hg19: chr6-140620884;