chr12-124607750-A-C

Variant names:

• chr12-124607750-A-C
• rs4765158
• ENST00000767262.1:n.309-1391T>G

Variant summary

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

The ENST00000767262.1(ENSG00000299894):​n.309-1391T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,040 control chromosomes in the GnomAD database, including 8,662 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 0.33 (8662 hom., cov: 34)
• Consequence: ENSG00000299894 ENST00000767262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 2 publications found

Genes affected

ENSG00000299894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767262.1. 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
	ENSG00000299894	ENST00000767262.1		n.309-1391T>G		intron	N/A
	ENSG00000299894	ENST00000767263.1		n.351+953T>G		intron	N/A
	ENSG00000299894	ENST00000767264.1		n.307+953T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49652 AN: 151922 Hom.: 8659 Cov.: 34

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.327 AC: 49655 AN: 152040 Hom.: 8662 Cov.: 34 AF XY: 0.321 AC XY: 23851 AN XY: 74320

African (AFR) AF: 0.215 AC: 8914 AN: 41488

American (AMR) AF: 0.293 AC: 4485 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2347 AN: 5164

South Asian (SAS) AF: 0.329 AC: 1588 AN: 4824

European-Finnish (FIN) AF: 0.277 AC: 2923 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26606 AN: 67944

Other (OTH) AF: 0.375 AC: 790 AN: 2106

Alfa AF: 0.379 Hom.: 22254

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		-0.54

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: rs4765158;

hg19: chr12-125092296;