chr12-93310184-G-A

Variant names:

• chr12-93310184-G-A
• rs930248
• ENST00000754393.1:n.323+17843C>T

Variant summary

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

The ENST00000754393.1(ENSG00000257252):​n.323+17843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,052 control chromosomes in the GnomAD database, including 13,756 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 0.40 (13756 hom., cov: 32)
• Consequence: ENSG00000257252 ENST00000754393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 5 publications found

Genes affected

ENSG00000257252 (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 (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643339	NR_040096.1	n.329+17843C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257252	ENST00000754393.1	n.323+17843C>T		intron_variant	Intron 2 of 7
ENSG00000257252	ENST00000754394.1	n.155+17843C>T		intron_variant	Intron 2 of 8
ENSG00000257252	ENST00000754396.1	n.232+5198C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61433 AN: 151934 Hom.: 13757 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.404 AC: 61429 AN: 152052 Hom.: 13756 Cov.: 32 AF XY: 0.403 AC XY: 29905 AN XY: 74296

African (AFR) AF: 0.209 AC: 8678 AN: 41502

American (AMR) AF: 0.345 AC: 5271 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2580 AN: 5156

South Asian (SAS) AF: 0.421 AC: 2032 AN: 4830

European-Finnish (FIN) AF: 0.518 AC: 5466 AN: 10544

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34139 AN: 67952

Other (OTH) AF: 0.431 AC: 913 AN: 2116

Alfa AF: 0.467 Hom.: 32051

Bravo AF: 0.384

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.51
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs930248; hg19: chr12-93703960;