ENST00000820282.1:n.594-8282A>G

Variant names:

• chr6-87933354-A-G
• rs4235835
• ENST00000820282.1:n.594-8282A>G

Variant summary

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

The ENST00000820282.1(ENSG00000306704):​n.594-8282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,074 control chromosomes in the GnomAD database, including 21,009 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 0.51 (21009 hom., cov: 32)
• Consequence: ENSG00000306704 ENST00000820282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 3 publications found

Genes affected

ENSG00000306704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377882	XR_001744246.1	n.203+1711A>G		intron_variant	Intron 1 of 2
LOC105377882	XR_002956400.1	n.203+1711A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306704	ENST00000820282.1	n.594-8282A>G		intron_variant	Intron 4 of 4
ENSG00000306704	ENST00000820285.1	n.608+1711A>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76974 AN: 151956 Hom.: 21024 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.506 AC: 76981 AN: 152074 Hom.: 21009 Cov.: 32 AF XY: 0.505 AC XY: 37537 AN XY: 74328

African (AFR) AF: 0.302 AC: 12535 AN: 41474

American (AMR) AF: 0.523 AC: 8001 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2212 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1739 AN: 5174

South Asian (SAS) AF: 0.531 AC: 2554 AN: 4806

European-Finnish (FIN) AF: 0.602 AC: 6363 AN: 10570

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41762 AN: 67978

Other (OTH) AF: 0.539 AC: 1136 AN: 2108

Alfa AF: 0.580 Hom.: 111035

Bravo AF: 0.491

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4235835; hg19: chr6-88643072;