chr12-27331677-TCTA-T

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902906	XR_007063255.1	n.176+942_176+944delTAG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304890	ENST00000806970.1	n.249+942_249+944delTAG		intron_variant	Intron 1 of 1
ENSG00000304890	ENST00000806971.1	n.233+942_233+944delTAG		intron_variant	Intron 1 of 2
ENSG00000304890	ENST00000806972.1	n.193+942_193+944delTAG		intron_variant	Intron 1 of 3

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 v4.3

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;