rs1879390

Variant names:

• chr12-127433587-C-A
• rs1879390
• ENST00000780743.1:n.158-4903C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-127433587-C-A
• chr12-127433587-C-G
• chr12-127433587-C-T

Variant summary

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

The ENST00000780743.1(ENSG00000301676):​n.158-4903C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,044 control chromosomes in the GnomAD database, including 1,613 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 0.14 (1613 hom., cov: 31)
• Consequence: ENSG00000301676 ENST00000780743.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 3 publications found

Genes affected

ENSG00000301676 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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
ENSG00000301676	ENST00000780743.1	n.158-4903C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21312 AN: 151926 Hom.: 1606 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.140 AC: 21359 AN: 152044 Hom.: 1613 Cov.: 31 AF XY: 0.143 AC XY: 10625 AN XY: 74306

African (AFR) AF: 0.192 AC: 7957 AN: 41456

American (AMR) AF: 0.121 AC: 1849 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.0381 AC: 196 AN: 5146

South Asian (SAS) AF: 0.174 AC: 836 AN: 4808

European-Finnish (FIN) AF: 0.150 AC: 1585 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8017 AN: 67992

Other (OTH) AF: 0.134 AC: 282 AN: 2112

Alfa AF: 0.120 Hom.: 2016

Bravo AF: 0.137

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.41
DANN	Benign	0.83
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1879390; hg19: chr12-127918132;