rs6585436

Positions:

• chr10-117450864-T-C

Variant summary

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

The ENST00000549104.1(ENSG00000258114):​n.268+14540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,324 control chromosomes in the GnomAD database, including 194 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 0.043 (194 hom., cov: 33)
• Consequence: ENSG00000258114 ENST00000549104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

ENSG00000258114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378502	XR_946344.1	n.95-4189T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258114	ENST00000549104.1	n.268+14540T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6515 AN: 152206 Hom.: 193 Cov.: 33

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.00913

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0428 AC: 6519 AN: 152324 Hom.: 194 Cov.: 33 AF XY: 0.0422 AC XY: 3145 AN XY: 74480

Gnomad4 AFR AF: 0.0687

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.0559

Gnomad4 FIN AF: 0.00913

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0332 Hom.: 246

Bravo AF: 0.0457

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6585436; hg19: chr10-119210375;