12-46962344-A-G

Variant names:

• chr12-46962344-A-G
• rs2250595
• ENST00000757663.1:n.236-7916A>G

Variant summary

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

The ENST00000757663.1(ENSG00000274723):​n.236-7916A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,026 control chromosomes in the GnomAD database, including 30,325 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 0.61 (30325 hom., cov: 31)
• Consequence: ENSG00000274723 ENST00000757663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 1 publications found

Genes affected

ENSG00000274723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757663.1. 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
	ENSG00000274723	ENST00000757663.1		n.236-7916A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92253 AN: 151908 Hom.: 30258 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.608 AC: 92387 AN: 152026 Hom.: 30325 Cov.: 31 AF XY: 0.606 AC XY: 45032 AN XY: 74318

African (AFR) AF: 0.838 AC: 34779 AN: 41490

American (AMR) AF: 0.701 AC: 10710 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1984 AN: 3466

East Asian (EAS) AF: 0.771 AC: 3981 AN: 5166

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3821 AN: 10560

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32296 AN: 67944

Other (OTH) AF: 0.606 AC: 1278 AN: 2108

Alfa AF: 0.513 Hom.: 12531

Bravo AF: 0.644

Asia WGS AF: 0.707 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		0.19

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: rs2250595;

hg19: chr12-47356127;