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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927436	XR_242964.4	n.443-108T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299894	ENST00000767262.1	n.309-1391T>G		intron_variant	Intron 2 of 3
ENSG00000299894	ENST00000767263.1	n.351+953T>G		intron_variant	Intron 2 of 3
ENSG00000299894	ENST00000767264.1	n.307+953T>G		intron_variant	Intron 1 of 2
ENSG00000299894	ENST00000767265.1	n.-148T>G		upstream_gene_variant

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 v4.3

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

Other links and lift over

dbSNP: rs4765158; hg19: chr12-125092296;