12-104424414-C-T

Variant names:

• chr12-104424414-C-T
• rs11112046
• ENST00000758099.1:n.251-6025C>T

Variant summary

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

The ENST00000758099.1(ENSG00000298817):​n.251-6025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 152,296 control chromosomes in the GnomAD database, including 430 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 0.059 (430 hom., cov: 32)
• Consequence: ENSG00000298817 ENST00000758099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 5 publications found

Genes affected

ENSG00000298817 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758099.1. 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
	ENSG00000298817	ENST00000758099.1		n.251-6025C>T		intron	N/A
	ENSG00000298817	ENST00000758100.1		n.265-6025C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8942 AN: 152178 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0588 AC: 8950 AN: 152296 Hom.: 430 Cov.: 32 AF XY: 0.0608 AC XY: 4526 AN XY: 74484

African (AFR) AF: 0.0189 AC: 785 AN: 41562

American (AMR) AF: 0.136 AC: 2083 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.178 AC: 923 AN: 5182

South Asian (SAS) AF: 0.0762 AC: 368 AN: 4828

European-Finnish (FIN) AF: 0.0603 AC: 640 AN: 10612

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

European-Non Finnish (NFE) AF: 0.0564 AC: 3838 AN: 68024

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0559 Hom.: 936

Bravo AF: 0.0632

Asia WGS AF: 0.115 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.41
PhyloP100		-0.40

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: rs11112046;

hg19: chr12-104818192;