12-96423644-A-G

Variant names:

• chr12-96423644-A-G
• rs2028385
• ENST00000548740.1:n.314-1253T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548740.1(ENSG00000258272):​n.314-1253T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,266 control chromosomes in the GnomAD database, including 3,126 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 0.20 (3126 hom., cov: 32)
• Consequence: ENSG00000258272 ENST00000548740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

ENSG00000258272 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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
ENSG00000258272	ENST00000548740.1	n.314-1253T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29729 AN: 152148 Hom.: 3113 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 29776 AN: 152266 Hom.: 3126 Cov.: 32 AF XY: 0.199 AC XY: 14821 AN XY: 74466

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.195

Alfa AF: 0.164 Hom.: 3014

Bravo AF: 0.203

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2028385; hg19: chr12-96817422;