12-131377862-G-T

Variant names:

• chr12-131377862-G-T
• rs7299374
• ENST00000833340.1:n.629-1997G>T

Variant summary

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

The ENST00000833340.1(ENSG00000308331):​n.629-1997G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,090 control chromosomes in the GnomAD database, including 1,219 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 (1219 hom., cov: 32)
• Consequence: ENSG00000308331 ENST00000833340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 2 publications found

Genes affected

ENSG00000308331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308331	ENST00000833340.1	n.629-1997G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17255 AN: 151972 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.114 AC: 17280 AN: 152090 Hom.: 1219 Cov.: 32 AF XY: 0.111 AC XY: 8231 AN XY: 74346

African (AFR) AF: 0.198 AC: 8228 AN: 41456

American (AMR) AF: 0.0706 AC: 1080 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0796 AC: 276 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0680 AC: 327 AN: 4806

European-Finnish (FIN) AF: 0.0970 AC: 1026 AN: 10572

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6073 AN: 67998

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0282 Hom.: 14

Bravo AF: 0.115

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	0.43
DANN	Benign	0.70
PhyloP100		-0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7299374; hg19: chr12-131862407;