10-6747501-C-T

Variant names:

• chr10-6747501-C-T
• rs12570744
• ENST00000648995.1:n.211+9873C>T

Variant summary

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

The ENST00000648995.1(ENSG00000285988):​n.211+9873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,082 control chromosomes in the GnomAD database, including 3,683 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 0.21 (3683 hom., cov: 32)
• Consequence: ENSG00000285988 ENST00000648995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

ENSG00000285988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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
ENSG00000285988	ENST00000648995.1	n.211+9873C>T		intron_variant	Intron 1 of 3
ENSG00000285743	ENST00000650342.1	n.375-33803C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31435 AN: 151964 Hom.: 3673 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.207 AC: 31481 AN: 152082 Hom.: 3683 Cov.: 32 AF XY: 0.211 AC XY: 15686 AN XY: 74338

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.204

Alfa AF: 0.193 Hom.: 6296

Bravo AF: 0.218

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12570744; hg19: chr10-6789463;