rs13208321

chr6-96412478-A-Gchr6-96412478-A-T

Variant summary

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

The ENST00000658843.2(UFL1-AS1):n.82-13444T>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 0.701 in 151,938 control chromosomes in the GnomAD database, including 38,882 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 0.70 (38882 hom., cov: 30)
• Consequence: UFL1-AS1 ENST00000658843.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UFL1-AS1	XR_007059687.1	n.9176-42998T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UFL1-AS1	ENST00000658843.2	n.82-13444T>C		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000430796.1	n.111-13444T>C		intron_variant, non_coding_transcript_variant		3
UFL1-AS1	ENST00000656359.1	n.175-13444T>C		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000662501.1	n.174-13444T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106425 AN: 151818 Hom.: 38858 Cov.: 30

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.701 AC: 106491 AN: 151938 Hom.: 38882 Cov.: 30 AF XY: 0.706 AC XY: 52429 AN XY: 74238

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.712

Alfa AF: 0.736 Hom.: 6637

Bravo AF: 0.689

Asia WGS AF: 0.798 AC: 2772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13208321; hg19: chr6-96860354;