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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830114.1. 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
	ENSG00000307967	ENST00000830114.1		n.120+2860G>A		intron	N/A
	ENSG00000307967	ENST00000830115.1		n.224+2860G>A		intron	N/A
	ENSG00000307967	ENST00000830116.1		n.353-1259G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs679090;

hg19: chr13-77547791;