12-47245743-T-C

Variant names:

• chr12-47245743-T-C
• rs11610206
• ENST00000547748.1:n.107-7453A>G

Variant summary

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

The ENST00000547748.1(ENSG00000257925):​n.107-7453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,310 control chromosomes in the GnomAD database, including 763 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 (763 hom., cov: 33)
• Consequence: ENSG00000257925 ENST00000547748.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 19 publications found

Genes affected

ENSG00000257925 (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 (EAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547748.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257925	ENST00000547748.1	TSL:2	n.107-7453A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14876 AN: 152192 Hom.: 763 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.0961

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

GnomAD4 genome AF: 0.0977 AC: 14883 AN: 152310 Hom.: 763 Cov.: 33 AF XY: 0.0978 AC XY: 7281 AN XY: 74484

African (AFR) AF: 0.120 AC: 4984 AN: 41566

American (AMR) AF: 0.0867 AC: 1327 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5184

South Asian (SAS) AF: 0.107 AC: 517 AN: 4822

European-Finnish (FIN) AF: 0.0803 AC: 853 AN: 10618

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0839 AC: 5709 AN: 68030

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0915 Hom.: 2249

Bravo AF: 0.101

Asia WGS AF: 0.111 AC: 387 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	1.9
DANN	Benign	0.35
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11610206; hg19: chr12-47639526;