12-107120863-A-G

Variant names:

• chr12-107120863-A-G
• rs1921141
• ENST00000547679.1:n.128-1110A>G

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.128-1110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,154 control chromosomes in the GnomAD database, including 10,162 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 0.36 (10162 hom., cov: 33)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.439 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.128-1110A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54769 AN: 152036 Hom.: 10151 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.360 AC: 54809 AN: 152154 Hom.: 10162 Cov.: 33 AF XY: 0.362 AC XY: 26955 AN XY: 74380

African (AFR) AF: 0.291 AC: 12070 AN: 41512

American (AMR) AF: 0.448 AC: 6850 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3466

East Asian (EAS) AF: 0.443 AC: 2295 AN: 5180

South Asian (SAS) AF: 0.389 AC: 1879 AN: 4826

European-Finnish (FIN) AF: 0.353 AC: 3735 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25444 AN: 67992

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.374 Hom.: 6386

Bravo AF: 0.366

Asia WGS AF: 0.356 AC: 1237 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.72
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1921141; hg19: chr12-107514641;