chr12-131381745-C-T

Variant names:

• chr12-131381745-C-T
• rs6486658
• ENST00000833460.1:n.184-1662G>A

Variant summary

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

The ENST00000833460.1(ENSG00000308352):​n.184-1662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,028 control chromosomes in the GnomAD database, including 1,481 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 0.12 (1481 hom., cov: 31)
• Consequence: ENSG00000308352 ENST00000833460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 4 publications found

Genes affected

ENSG00000308352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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
ENSG00000308352	ENST00000833460.1	n.184-1662G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18703 AN: 151910 Hom.: 1479 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.123 AC: 18723 AN: 152028 Hom.: 1481 Cov.: 31 AF XY: 0.121 AC XY: 9010 AN XY: 74322

African (AFR) AF: 0.223 AC: 9227 AN: 41442

American (AMR) AF: 0.0731 AC: 1118 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5162

South Asian (SAS) AF: 0.0715 AC: 345 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6162 AN: 67952

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.0975 Hom.: 438

Bravo AF: 0.124

Asia WGS AF: 0.0410 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.86
DANN	Benign	0.68
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6486658; hg19: chr12-131866290;