ENST00000844184.1:n.164-17794G>T

Variant names:

• chr12-65140844-C-A
• rs6581612
• ENST00000844184.1:n.164-17794G>T

Variant summary

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

The ENST00000844184.1(ENSG00000289319):​n.164-17794G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 151,998 control chromosomes in the GnomAD database, including 40,968 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 0.73 (40968 hom., cov: 31)
• Consequence: ENSG00000289319 ENST00000844184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 23 publications found

Genes affected

ENSG00000289319 (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 (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
ENSG00000289319	ENST00000844184.1	n.164-17794G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111190 AN: 151880 Hom.: 40936 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.732 AC: 111269 AN: 151998 Hom.: 40968 Cov.: 31 AF XY: 0.739 AC XY: 54913 AN XY: 74296

African (AFR) AF: 0.661 AC: 27389 AN: 41432

American (AMR) AF: 0.717 AC: 10938 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2691 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5161 AN: 5178

South Asian (SAS) AF: 0.856 AC: 4119 AN: 4814

European-Finnish (FIN) AF: 0.764 AC: 8068 AN: 10566

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50437 AN: 67972

Other (OTH) AF: 0.767 AC: 1616 AN: 2106

Alfa AF: 0.747 Hom.: 176174

Bravo AF: 0.725

Asia WGS AF: 0.915 AC: 3177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6581612; hg19: chr12-65534624;