rs10509309

Variant names:

• chr10-69067525-T-C
• rs10509309
• ENST00000746576.1:n.574-2570T>C

Variant summary

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

The ENST00000746576.1(ENSG00000297252):​n.574-2570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,984 control chromosomes in the GnomAD database, including 9,450 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 0.35 (9450 hom., cov: 31)
• Consequence: ENSG00000297252 ENST00000746576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 11 publications found

Genes affected

ENSG00000297252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746576.1. 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
	ENSG00000297252	ENST00000746576.1		n.574-2570T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52924 AN: 151866 Hom.: 9431 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.349 AC: 52992 AN: 151984 Hom.: 9450 Cov.: 31 AF XY: 0.346 AC XY: 25675 AN XY: 74290

African (AFR) AF: 0.396 AC: 16412 AN: 41430

American (AMR) AF: 0.283 AC: 4318 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1104 AN: 5180

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3750 AN: 10560

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23761 AN: 67960

Other (OTH) AF: 0.319 AC: 671 AN: 2104

Alfa AF: 0.341 Hom.: 15455

Bravo AF: 0.343

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10509309; hg19: chr10-70827281;