12-91454361-T-C

Variant names:

• chr12-91454361-T-C
• rs2034954
• ENST00000685093.1:n.674+52350A>G

Variant summary

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

The ENST00000685093.1(ENSG00000289605):​n.674+52350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,938 control chromosomes in the GnomAD database, including 14,749 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 0.44 (14749 hom., cov: 32)
• Consequence: ENSG00000289605 ENST00000685093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 2 publications found

Genes affected

ENSG00000289605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685093.1. 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
	ENSG00000289605	ENST00000685093.1		n.674+52350A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66516 AN: 151818 Hom.: 14734 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.438 AC: 66582 AN: 151938 Hom.: 14749 Cov.: 32 AF XY: 0.434 AC XY: 32218 AN XY: 74244

African (AFR) AF: 0.411 AC: 17017 AN: 41430

American (AMR) AF: 0.434 AC: 6617 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1999 AN: 5162

South Asian (SAS) AF: 0.395 AC: 1906 AN: 4826

European-Finnish (FIN) AF: 0.414 AC: 4357 AN: 10530

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31889 AN: 67950

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.437 Hom.: 5435

Bravo AF: 0.439

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2034954; hg19: chr12-91848138;