rs780873

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-115757976-G-A
• chr12-115757976-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370003	XR_945388.3	n.118+4972C>T		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.118+4972C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257781	ENST00000549163.1	n.129+2586G>A		intron_variant	Intron 1 of 2	3
ENSG00000257781	ENST00000825498.1	n.363+7040G>A		intron_variant	Intron 1 of 1
ENSG00000257781	ENST00000825499.1	n.192+2586G>A		intron_variant	Intron 1 of 2
ENSG00000257781	ENST00000825500.1	n.-207G>A		upstream_gene_variant

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 v4.3

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;