rs10861709

Variant names:

• chr12-107111862-C-T
• rs10861709
• ENST00000547679.1:n.128-10111C>T

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.128-10111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,986 control chromosomes in the GnomAD database, including 19,771 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 0.50 (19771 hom., cov: 32)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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
ENSG00000257548	ENST00000547679.1	n.128-10111C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75220 AN: 151868 Hom.: 19756 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.495 AC: 75267 AN: 151986 Hom.: 19771 Cov.: 32 AF XY: 0.499 AC XY: 37096 AN XY: 74286

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.517

Alfa AF: 0.554 Hom.: 31763

Bravo AF: 0.493

Asia WGS AF: 0.596 AC: 2072 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861709; hg19: chr12-107505640;