rs1793584

Variant names:

• chr11-131303980-G-A
• rs1793584
• ENST00000606885.1:n.147-46329G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-131303980-G-A
• chr11-131303980-G-C

Variant summary

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

The ENST00000606885.1(ENSG00000231698):​n.147-46329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,166 control chromosomes in the GnomAD database, including 3,216 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 0.20 (3216 hom., cov: 33)
• Consequence: ENSG00000231698 ENST00000606885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

ENSG00000231698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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
ENSG00000231698	ENST00000606885.1	n.147-46329G>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30379 AN: 152048 Hom.: 3203 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30417 AN: 152166 Hom.: 3216 Cov.: 33 AF XY: 0.199 AC XY: 14805 AN XY: 74384

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.205

Alfa AF: 0.204 Hom.: 537

Bravo AF: 0.212

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1793584; hg19: chr11-131173875;