rs11156352

Positions:

• chr6-96239646-A-G

Variant summary

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

The ENST00000658843.2(UFL1-AS1):​n.302-36631T>C 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 0.13 in 152,200 control chromosomes in the GnomAD database, including 1,558 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 0.13 (1558 hom., cov: 32)
• Consequence: UFL1-AS1 ENST00000658843.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

Genes affected

UFL1-AS1 (HGNC:41007): (UFL1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UFL1-AS1	XR_007059687.1	n.9276-36631T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UFL1-AS1	ENST00000658843.2	n.302-36631T>C		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000662501.1	n.394-36631T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19805 AN: 152082 Hom.: 1557 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.130 AC: 19808 AN: 152200 Hom.: 1558 Cov.: 32 AF XY: 0.126 AC XY: 9411 AN XY: 74416

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.127

Alfa AF: 0.158 Hom.: 721

Bravo AF: 0.129

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11156352; hg19: chr6-96687522;