rs679090

Variant names:

• chr13-76973656-C-T
• rs679090
• ENST00000830114.1:n.120+2860G>A

Variant summary

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

The ENST00000830114.1(ENSG00000307967):​n.120+2860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,112 control chromosomes in the GnomAD database, including 46,981 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 0.78 (46981 hom., cov: 32)
• Consequence: ENSG00000307967 ENST00000830114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 2 publications found

Genes affected

ENSG00000307967 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370269	XR_001749929.1	n.212+2860G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307967	ENST00000830114.1	n.120+2860G>A		intron_variant	Intron 1 of 3
ENSG00000307967	ENST00000830115.1	n.224+2860G>A		intron_variant	Intron 2 of 2
ENSG00000307967	ENST00000830116.1	n.353-1259G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118676 AN: 151994 Hom.: 46958 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.781 AC: 118746 AN: 152112 Hom.: 46981 Cov.: 32 AF XY: 0.770 AC XY: 57227 AN XY: 74342

African (AFR) AF: 0.780 AC: 32344 AN: 41490

American (AMR) AF: 0.772 AC: 11796 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2904 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2424 AN: 5162

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4820

European-Finnish (FIN) AF: 0.759 AC: 8013 AN: 10558

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56152 AN: 68012

Other (OTH) AF: 0.789 AC: 1665 AN: 2110

Alfa AF: 0.805 Hom.: 92372

Bravo AF: 0.785

Asia WGS AF: 0.486 AC: 1692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.76
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs679090; hg19: chr13-77547791;