13-44889012-T-A

Variant names:

• chr13-44889012-T-A
• rs10492743
• ENST00000807128.1:n.295-845A>T

Variant summary

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

The ENST00000807128.1(ENSG00000304924):​n.295-845A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,048 control chromosomes in the GnomAD database, including 33,134 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 0.65 (33134 hom., cov: 31)
• Consequence: ENSG00000304924 ENST00000807128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 3 publications found

Genes affected

ENSG00000304924 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807128.1. 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
	ENSG00000304924	ENST00000807128.1		n.295-845A>T		intron	N/A
	ENSG00000304924	ENST00000807129.1		n.298-845A>T		intron	N/A
	ENSG00000304924	ENST00000807130.1		n.264-845A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98456 AN: 151930 Hom.: 33112 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.648 AC: 98507 AN: 152048 Hom.: 33134 Cov.: 31 AF XY: 0.657 AC XY: 48835 AN XY: 74330

African (AFR) AF: 0.454 AC: 18808 AN: 41446

American (AMR) AF: 0.760 AC: 11616 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4593 AN: 5164

South Asian (SAS) AF: 0.773 AC: 3713 AN: 4804

European-Finnish (FIN) AF: 0.728 AC: 7700 AN: 10576

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47390 AN: 67992

Other (OTH) AF: 0.659 AC: 1393 AN: 2114

Alfa AF: 0.597 Hom.: 2052

Bravo AF: 0.641

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs10492743; hg19: chr13-45463147;