12-30824421-A-C

Variant names:

• chr12-30824421-A-C
• rs33149
• ENST00000648700.1:n.246+24400A>C

Variant summary

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

The ENST00000648700.1(ENSG00000285517):​n.246+24400A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,892 control chromosomes in the GnomAD database, including 39,174 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 0.71 (39174 hom., cov: 30)
• Consequence: ENSG00000285517 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

Genes affected

ENSG00000285517 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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
ENSG00000285517	ENST00000648700.1	n.246+24400A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108157 AN: 151776 Hom.: 39164 Cov.: 30

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.712 AC: 108204 AN: 151892 Hom.: 39174 Cov.: 30 AF XY: 0.713 AC XY: 52938 AN XY: 74214

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.712

Alfa AF: 0.730 Hom.: 86117

Bravo AF: 0.694

Asia WGS AF: 0.895 AC: 3110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33149; hg19: chr12-30977355;