rs1881744

Variant names:

• chr12-47421189-G-A
• rs1881744
• ENST00000848642.1:n.511-2932C>T

Variant summary

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

The ENST00000848642.1(ENSG00000310270):​n.511-2932C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,198 control chromosomes in the GnomAD database, including 406 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 0.067 (406 hom., cov: 31)
• Consequence: ENSG00000310270 ENST00000848642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

ENSG00000310270 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0885 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
ENSG00000310270	ENST00000848642.1	n.511-2932C>T		intron_variant	Intron 1 of 1
ENSG00000310270	ENST00000848643.1	n.531-2816C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10156 AN: 152080 Hom.: 408 Cov.: 31

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0667 AC: 10148 AN: 152198 Hom.: 406 Cov.: 31 AF XY: 0.0642 AC XY: 4780 AN XY: 74422

African (AFR) AF: 0.0269 AC: 1116 AN: 41546

American (AMR) AF: 0.0844 AC: 1290 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3470

East Asian (EAS) AF: 0.0189 AC: 98 AN: 5186

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4818

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10600

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0904 AC: 6143 AN: 67988

Other (OTH) AF: 0.0875 AC: 184 AN: 2104

Alfa AF: 0.0776 Hom.: 765

Bravo AF: 0.0668

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1881744; hg19: chr12-47814972;