chr10-113989376-G-T

Variant names:

• chr10-113989376-G-T
• rs6585258
• ENST00000751600.1:n.324-4720G>T

Variant summary

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

The ENST00000751600.1(ENSG00000297898):​n.324-4720G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,578 control chromosomes in the GnomAD database, including 15,620 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 0.45 (15620 hom., cov: 32)
• Consequence: ENSG00000297898 ENST00000751600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 4 publications found

Genes affected

ENSG00000297898 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 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
ENSG00000297898	ENST00000751600.1	n.324-4720G>T		intron_variant	Intron 2 of 2
ENSG00000297898	ENST00000751601.1	n.256-1997G>T		intron_variant	Intron 2 of 3
ENSG00000297898	ENST00000751602.1	n.62-1997G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68458 AN: 151460 Hom.: 15604 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.452 AC: 68521 AN: 151578 Hom.: 15620 Cov.: 32 AF XY: 0.455 AC XY: 33699 AN XY: 74058

African (AFR) AF: 0.498 AC: 20611 AN: 41370

American (AMR) AF: 0.482 AC: 7336 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3464

East Asian (EAS) AF: 0.343 AC: 1770 AN: 5164

South Asian (SAS) AF: 0.511 AC: 2458 AN: 4812

European-Finnish (FIN) AF: 0.484 AC: 5033 AN: 10402

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28780 AN: 67826

Other (OTH) AF: 0.436 AC: 919 AN: 2106

Alfa AF: 0.435 Hom.: 7184

Bravo AF: 0.451

Asia WGS AF: 0.474 AC: 1617 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.14
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6585258; hg19: chr10-115749135;