12-16904489-T-G

Variant names:

• chr12-16904489-T-G
• rs978561
• ENST00000759187.1:n.353-28047A>C

Variant summary

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

The ENST00000759187.1(ENSG00000298941):​n.353-28047A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,932 control chromosomes in the GnomAD database, including 26,195 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 0.58 (26195 hom., cov: 32)
• Consequence: ENSG00000298941 ENST00000759187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87
• Publications: 2 publications found

Genes affected

ENSG00000298941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759187.1. 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
	ENSG00000298941	ENST00000759187.1		n.353-28047A>C		intron	N/A
	ENSG00000298941	ENST00000759188.1		n.608-4318A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87974 AN: 151814 Hom.: 26170 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.580 AC: 88051 AN: 151932 Hom.: 26195 Cov.: 32 AF XY: 0.581 AC XY: 43104 AN XY: 74228

African (AFR) AF: 0.719 AC: 29820 AN: 41480

American (AMR) AF: 0.594 AC: 9068 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1990 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3524 AN: 5132

South Asian (SAS) AF: 0.595 AC: 2859 AN: 4802

European-Finnish (FIN) AF: 0.484 AC: 5105 AN: 10556

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33859 AN: 67916

Other (OTH) AF: 0.602 AC: 1271 AN: 2110

Alfa AF: 0.534 Hom.: 86176

Bravo AF: 0.596

Asia WGS AF: 0.627 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.31
PhyloP100		-2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs978561;

hg19: chr12-17057423;