ENST00000549163.1:n.129+2586G>A

Variant names:

• chr12-115757976-G-A
• rs780873
• ENST00000549163.1:n.129+2586G>A

Variant summary

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

The ENST00000549163.1(ENSG00000257781):​n.129+2586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,232 control chromosomes in the GnomAD database, including 67,205 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 0.94 (67205 hom., cov: 32)
• Consequence: ENSG00000257781 ENST00000549163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 5 publications found

Genes affected

ENSG00000257781 (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 = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549163.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257781	ENST00000549163.1	TSL:3	n.129+2586G>A		intron	N/A
	ENSG00000257781	ENST00000825498.1		n.363+7040G>A		intron	N/A
	ENSG00000257781	ENST00000825499.1		n.192+2586G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142822 AN: 152114 Hom.: 67157 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.939 AC: 142928 AN: 152232 Hom.: 67205 Cov.: 32 AF XY: 0.940 AC XY: 69973 AN XY: 74436

African (AFR) AF: 0.888 AC: 36865 AN: 41512

American (AMR) AF: 0.958 AC: 14639 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3198 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5184

South Asian (SAS) AF: 0.959 AC: 4620 AN: 4816

European-Finnish (FIN) AF: 0.992 AC: 10537 AN: 10618

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64743 AN: 68024

Other (OTH) AF: 0.937 AC: 1983 AN: 2116

Alfa AF: 0.947 Hom.: 150000

Bravo AF: 0.937

Asia WGS AF: 0.978 AC: 3399 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	4.6
DANN	Benign	0.47
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs780873; hg19: chr12-116195781;