rs6585436

Variant names:

• chr10-117450864-T-C
• rs6585436
• ENST00000549104.1:n.268+14540T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000258114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258114	ENST00000549104.1	TSL:4	n.268+14540T>C		intron	N/A
	ENSG00000258114	ENST00000821096.1		n.270-4189T>C		intron	N/A
	ENSG00000258114	ENST00000821097.1		n.273-4535T>C		intron	N/A

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

African (AFR) AF: 0.0687 AC: 2854 AN: 41556

American (AMR) AF: 0.0337 AC: 516 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3470

East Asian (EAS) AF: 0.0864 AC: 448 AN: 5186

South Asian (SAS) AF: 0.0559 AC: 270 AN: 4828

European-Finnish (FIN) AF: 0.00913 AC: 97 AN: 10620

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0257 AC: 1750 AN: 68042

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0353 Hom.: 438

Bravo AF: 0.0457

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6585436;

hg19: chr10-119210375;