rs1806506

Positions:

• chr4-111546095-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681880.1(ENSG00000248656):​n.170+29809A>G variant causes a intron, non coding transcript 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: ENST00000681880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000681880.1	n.170+29809A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.645

Alfa AF: 0.592 Hom.: 54320

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1806506; hg19: chr4-112467251;