rs10512574

Variant names:

• chr17-70341823-T-C
• rs10512574
• ENST00000592809.1:n.102-8233A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-70341823-T-C
• chr17-70341823-T-G

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.102-8233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,250 control chromosomes in the GnomAD database, including 2,452 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 (2452 hom., cov: 33)
• Consequence: ENSG00000267109 ENST00000592809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 13 publications found

Genes affected

ENSG00000267109 (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 (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267109	ENST00000592809.1	TSL:3	n.102-8233A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25965 AN: 152132 Hom.: 2448 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.171 AC: 25980 AN: 152250 Hom.: 2452 Cov.: 33 AF XY: 0.171 AC XY: 12727 AN XY: 74440

African (AFR) AF: 0.109 AC: 4534 AN: 41562

American (AMR) AF: 0.200 AC: 3053 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3470

East Asian (EAS) AF: 0.165 AC: 854 AN: 5176

South Asian (SAS) AF: 0.230 AC: 1112 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10600

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13248 AN: 68006

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.190 Hom.: 3692

Bravo AF: 0.171

Asia WGS AF: 0.211 AC: 734 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	2.7
DANN	Benign	0.40
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10512574; hg19: chr17-68337964;