12-107097814-A-G

Variant names:

• chr12-107097814-A-G
• rs10861704
• ENST00000547679.1:n.127+344A>G

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,882 control chromosomes in the GnomAD database, including 20,248 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 (20248 hom., cov: 30)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257548	ENST00000547679.1	TSL:3	n.127+344A>G		intron	N/A
	ENSG00000257548	ENST00000817321.1		n.395+344A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76447 AN: 151764 Hom.: 20223 Cov.: 30

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.504 AC: 76520 AN: 151882 Hom.: 20248 Cov.: 30 AF XY: 0.508 AC XY: 37689 AN XY: 74208

African (AFR) AF: 0.337 AC: 13960 AN: 41404

American (AMR) AF: 0.591 AC: 9024 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3717 AN: 5142

South Asian (SAS) AF: 0.577 AC: 2772 AN: 4808

European-Finnish (FIN) AF: 0.512 AC: 5394 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38306 AN: 67934

Other (OTH) AF: 0.519 AC: 1097 AN: 2112

Alfa AF: 0.548 Hom.: 31412

Bravo AF: 0.503

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.37
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10861704; hg19: chr12-107491592;