chr6-96412478-A-G

Variant names:

• chr6-96412478-A-G
• rs13208321
• ENST00000430796.1:n.111-13444T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430796.1(UFL1-AS1):​n.111-13444T>C variant causes a intron 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 ENST00000430796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430796.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UFL1-AS1	ENST00000430796.1	TSL:3	n.111-13444T>C		intron	N/A
	UFL1-AS1	ENST00000656359.1		n.175-13444T>C		intron	N/A
	UFL1-AS1	ENST00000658843.2		n.82-13444T>C		intron	N/A

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

African (AFR) AF: 0.476 AC: 19744 AN: 41448

American (AMR) AF: 0.778 AC: 11862 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2737 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4704 AN: 5130

South Asian (SAS) AF: 0.775 AC: 3730 AN: 4812

European-Finnish (FIN) AF: 0.817 AC: 8647 AN: 10586

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.776 AC: 52699 AN: 67938

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.729 Hom.: 6737

Bravo AF: 0.689

Asia WGS AF: 0.798 AC: 2772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.70
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs13208321; hg19: chr6-96860354;