ENST00000824449.1:n.594-1426T>C

Variant names:

• chr20-56661502-A-G
• rs6014787
• ENST00000824449.1:n.594-1426T>C

Variant summary

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

The ENST00000824449.1(ENSG00000307191):​n.594-1426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,070 control chromosomes in the GnomAD database, including 15,491 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 0.40 (15491 hom., cov: 32)
• Consequence: ENSG00000307191 ENST00000824449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 3 publications found

Genes affected

ENSG00000307191 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824449.1. 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
	ENSG00000307191	ENST00000824449.1		n.594-1426T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61433 AN: 151952 Hom.: 15449 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.405 AC: 61523 AN: 152070 Hom.: 15491 Cov.: 32 AF XY: 0.399 AC XY: 29649 AN XY: 74328

African (AFR) AF: 0.704 AC: 29198 AN: 41486

American (AMR) AF: 0.292 AC: 4450 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5180

South Asian (SAS) AF: 0.207 AC: 995 AN: 4814

European-Finnish (FIN) AF: 0.326 AC: 3443 AN: 10564

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20957 AN: 67990

Other (OTH) AF: 0.381 AC: 800 AN: 2098

Alfa AF: 0.322 Hom.: 13093

Bravo AF: 0.415

Asia WGS AF: 0.147 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs6014787; hg19: chr20-55236558;