rs11729080

Variant names:

• chr4-111582716-G-A
• rs11729080
• ENST00000681880.1:n.171-35789G>A

Variant summary

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

The ENST00000681880.1(ENSG00000248656):​n.171-35789G>A 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 152,188 control chromosomes in the GnomAD database, including 1,149 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 (1149 hom., cov: 32)
• Consequence: ENSG00000248656 ENST00000681880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 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.171-35789G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15878 AN: 152070 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.104 AC: 15866 AN: 152188 Hom.: 1149 Cov.: 32 AF XY: 0.102 AC XY: 7602 AN XY: 74384

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.143 Hom.: 1073

Bravo AF: 0.0949

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11729080; hg19: chr4-112503872;