ENST00000681880.1:n.170+29809A>G

Variant names:

• chr4-111546095-A-G
• rs1806506
• ENST00000681880.1:n.170+29809A>G

Variant summary

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

The ENST00000681880.1(ENSG00000248656):​n.170+29809A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,982 control chromosomes in the GnomAD database, including 30,038 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 0.62 (30038 hom., cov: 32)
• Consequence: ENSG00000248656 ENST00000681880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 3 publications found

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248656	ENST00000681880.1	n.170+29809A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94604 AN: 151864 Hom.: 30000 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.623 AC: 94703 AN: 151982 Hom.: 30038 Cov.: 32 AF XY: 0.624 AC XY: 46347 AN XY: 74280

African (AFR) AF: 0.687 AC: 28472 AN: 41436

American (AMR) AF: 0.643 AC: 9808 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4307 AN: 5172

South Asian (SAS) AF: 0.682 AC: 3287 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5452 AN: 10554

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.576 AC: 39178 AN: 67972

Other (OTH) AF: 0.645 AC: 1357 AN: 2104

Alfa AF: 0.595 Hom.: 116340

Bravo AF: 0.634

Asia WGS AF: 0.711 AC: 2470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.50
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1806506; hg19: chr4-112467251;