rs10484713

Positions:

• chr6-140299747-C-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, non coding transcript 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: ENST00000683950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000683950.1	n.202-15083C>T		intron_variant, non_coding_transcript_variant

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;