6-90909043-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1349+882A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307789	ENST00000828793.1	n.281+882A>G		intron_variant	Intron 2 of 3
ENSG00000307789	ENST00000828794.1	n.516+882A>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs13220542; hg19: chr6-91618761;