rs10548381

Variant names:

• chr12-27331677-TCTA-T
• rs10548381
• ENST00000806970.1:n.249+942_249+944delTAG

Your query was ambiguous. Multiple possible variants found:

• chr12-27331677-TCTA-T
• chr12-27331677-TCTA-TCTACTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000806970.1(ENSG00000304890):​n.249+942_249+944delTAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,252 control chromosomes in the GnomAD database, including 517 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (517 hom., cov: 30)
• Consequence: ENSG00000304890 ENST00000806970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 3 publications found

Genes affected

ENSG00000304890 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304890	ENST00000806970.1		n.249+942_249+944delTAG		intron	N/A
	ENSG00000304890	ENST00000806971.1		n.233+942_233+944delTAG		intron	N/A
	ENSG00000304890	ENST00000806972.1		n.193+942_193+944delTAG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11876 AN: 152134 Hom.: 517 Cov.: 30

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0780 AC: 11876 AN: 152252 Hom.: 517 Cov.: 30 AF XY: 0.0773 AC XY: 5754 AN XY: 74448

African (AFR) AF: 0.0425 AC: 1768 AN: 41558

American (AMR) AF: 0.0534 AC: 817 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5188

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1115 AN: 10586

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7165 AN: 68012

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.103 Hom.: 110

Bravo AF: 0.0710

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10548381; hg19: chr12-27484610;