rs13220542

Variant names:

• chr6-90909043-A-G
• rs13220542
• ENST00000828793.1:n.281+882A>G

Variant summary

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

The ENST00000828793.1(ENSG00000307789):​n.281+882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,216 control chromosomes in the GnomAD database, including 894 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 0.10 (894 hom., cov: 32)
• Consequence: ENSG00000307789 ENST00000828793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 2 publications found

Genes affected

ENSG00000307789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828793.1. 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
	ENSG00000307789	ENST00000828793.1		n.281+882A>G		intron	N/A
	ENSG00000307789	ENST00000828794.1		n.516+882A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15847 AN: 152098 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 15849 AN: 152216 Hom.: 894 Cov.: 32 AF XY: 0.107 AC XY: 7993 AN XY: 74404

African (AFR) AF: 0.0899 AC: 3733 AN: 41526

American (AMR) AF: 0.121 AC: 1854 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1080 AN: 5178

South Asian (SAS) AF: 0.153 AC: 736 AN: 4818

European-Finnish (FIN) AF: 0.119 AC: 1257 AN: 10602

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6645 AN: 68026

Other (OTH) AF: 0.110 AC: 233 AN: 2116

Alfa AF: 0.0968 Hom.: 107

Bravo AF: 0.104

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		0.018

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: rs13220542;

hg19: chr6-91618761;