chr12-93358310-C-T

Variant names:

• chr12-93358310-C-T
• rs4761708
• ENST00000548890.2:n.317+19127G>A

Variant summary

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

The ENST00000548890.2(ENSG00000257252):​n.317+19127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,998 control chromosomes in the GnomAD database, including 4,294 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 0.23 (4294 hom., cov: 31)
• Consequence: ENSG00000257252 ENST00000548890.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643339	NR_040096.1	n.300+19127G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257252	ENST00000548890.2	n.317+19127G>A		intron_variant	Intron 1 of 2	5
ENSG00000257252	ENST00000549806.2	n.335+19127G>A		intron_variant	Intron 1 of 1	5
ENSG00000257252	ENST00000552835.5	n.281-18574G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35660 AN: 151880 Hom.: 4280 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.235 AC: 35679 AN: 151998 Hom.: 4294 Cov.: 31 AF XY: 0.237 AC XY: 17612 AN XY: 74280

African (AFR) AF: 0.197 AC: 8167 AN: 41452

American (AMR) AF: 0.288 AC: 4403 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5162

South Asian (SAS) AF: 0.199 AC: 960 AN: 4816

European-Finnish (FIN) AF: 0.286 AC: 3016 AN: 10548

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16212 AN: 67966

Other (OTH) AF: 0.220 AC: 464 AN: 2106

Alfa AF: 0.238 Hom.: 17606

Bravo AF: 0.236

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.4
DANN	Benign	0.76
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs4761708; hg19: chr12-93752086;