rs10861709

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547679.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257548	ENST00000547679.1	TSL:3	n.128-10111C>T		intron	N/A

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

African (AFR) AF: 0.310 AC: 12825 AN: 41424

American (AMR) AF: 0.586 AC: 8952 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3753 AN: 5178

South Asian (SAS) AF: 0.568 AC: 2736 AN: 4820

European-Finnish (FIN) AF: 0.512 AC: 5396 AN: 10542

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.563 AC: 38272 AN: 67976

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.548 Hom.: 39192

Bravo AF: 0.493

Asia WGS AF: 0.596 AC: 2072 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.81
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs10861709; hg19: chr12-107505640;