6-96437010-G-A

Variant names:

• chr6-96437010-G-A
• rs11757063
• ENST00000430796.1:n.111-37976C>T

Variant summary

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

The ENST00000430796.1(UFL1-AS1):​n.111-37976C>T variant causes a intron 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 ENST00000430796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 20 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UFL1-AS1	ENST00000430796.1	TSL:3	n.111-37976C>T		intron	N/A
	UFL1-AS1	ENST00000656359.1		n.174+23430C>T		intron	N/A
	UFL1-AS1	ENST00000658843.2		n.82-37976C>T		intron	N/A

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

African (AFR) AF: 0.103 AC: 4284 AN: 41512

American (AMR) AF: 0.157 AC: 2402 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3466

East Asian (EAS) AF: 0.0446 AC: 230 AN: 5158

South Asian (SAS) AF: 0.180 AC: 865 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1276 AN: 10580

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12979 AN: 67970

Other (OTH) AF: 0.176 AC: 371 AN: 2104

Alfa AF: 0.176 Hom.: 4629

Bravo AF: 0.154

Asia WGS AF: 0.115 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11757063; hg19: chr6-96884886;