12-121104028-C-T

Variant names:

• chr12-121104028-C-T
• rs7298521
• ENST00000837362.1:n.128-3299G>A

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.128-3299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,184 control chromosomes in the GnomAD database, including 1,591 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 0.11 (1591 hom., cov: 34)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 3 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837362.1. 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
	ENSG00000308932	ENST00000837362.1		n.128-3299G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16531 AN: 152066 Hom.: 1586 Cov.: 34

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.109 AC: 16557 AN: 152184 Hom.: 1591 Cov.: 34 AF XY: 0.110 AC XY: 8206 AN XY: 74416

African (AFR) AF: 0.236 AC: 9770 AN: 41450

American (AMR) AF: 0.0468 AC: 715 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1360 AN: 5184

South Asian (SAS) AF: 0.126 AC: 610 AN: 4830

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0434 AC: 2950 AN: 68030

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0613 Hom.: 2417

Bravo AF: 0.110

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.94

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: rs7298521;

hg19: chr12-121541831;