rs11729080

Positions:

• chr4-111582716-G-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, non coding transcript 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: ENST00000681880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000681880.1	n.171-35789G>A		intron_variant, non_coding_transcript_variant

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;