10-71007652-T-C

Variant names:

• chr10-71007652-T-C
• rs10509328
• ENST00000646051.1:n.259-18927T>C

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.259-18927T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,178 control chromosomes in the GnomAD database, including 788 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 0.098 (788 hom., cov: 33)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 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
ENSG00000285300	ENST00000646051.1	n.259-18927T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14948 AN: 152060 Hom.: 785 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0984 AC: 14975 AN: 152178 Hom.: 788 Cov.: 33 AF XY: 0.0971 AC XY: 7226 AN XY: 74414

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0878 Hom.: 837

Bravo AF: 0.103

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509328; hg19: chr10-72767409;