rs11757063

Positions:

• chr6-96437010-G-A

Variant summary

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

The ENST00000658843.2(UFL1-AS1):​n.82-37976C>T 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 0.154 in 152,086 control chromosomes in the GnomAD database, including 1,945 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 0.15 (1945 hom., cov: 32)
• Consequence: UFL1-AS1 ENST00000658843.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UFL1-AS1	XR_007059687.1	n.9176-67530C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UFL1-AS1	ENST00000658843.2	n.82-37976C>T		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000430796.1	n.111-37976C>T		intron_variant, non_coding_transcript_variant		3
UFL1-AS1	ENST00000656359.1	n.174+23430C>T		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000662501.1	n.173+23476C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23390 AN: 151968 Hom.: 1947 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.154 AC: 23383 AN: 152086 Hom.: 1945 Cov.: 32 AF XY: 0.151 AC XY: 11231 AN XY: 74354

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0446

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.176

Alfa AF: 0.175 Hom.: 1334

Bravo AF: 0.154

Asia WGS AF: 0.115 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
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: rs11757063; hg19: chr6-96884886;