rs589636

Variant names:

• chr13-76942441-T-C
• rs589636
• ENST00000830115.1:n.655A>G

Variant summary

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

The ENST00000830115.1(ENSG00000307967):​n.655A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,154 control chromosomes in the GnomAD database, including 50,807 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 0.82 (50807 hom., cov: 32)
• Consequence: ENSG00000307967 ENST00000830115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830115.1. 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	ENST00000830115.1		n.655A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000307967	ENST00000830116.1		n.912A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000307967	ENST00000830117.1		n.695A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123962 AN: 152038 Hom.: 50782 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.815 AC: 124040 AN: 152154 Hom.: 50807 Cov.: 32 AF XY: 0.809 AC XY: 60180 AN XY: 74378

African (AFR) AF: 0.798 AC: 33126 AN: 41500

American (AMR) AF: 0.865 AC: 13228 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3091 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3928 AN: 5178

South Asian (SAS) AF: 0.551 AC: 2653 AN: 4818

European-Finnish (FIN) AF: 0.788 AC: 8329 AN: 10566

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56941 AN: 68010

Other (OTH) AF: 0.824 AC: 1743 AN: 2116

Alfa AF: 0.829 Hom.: 29100

Bravo AF: 0.825

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.46
PhyloP100		-2.7

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: rs589636;

hg19: chr13-77516576;