rs1328867

Positions:

• chr6-8652454-A-G

Variant summary

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

The ENST00000646741.1(HULC):​n.193A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,150 control chromosomes in the GnomAD database, including 15,059 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 0.44 (15053 hom., cov: 32)
  • Exomes 𝑓: 0.38 (6 hom.)
• Consequence: HULC ENST00000646741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

HULC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HULC	NR_004855.3	n.122+64A>G		intron_variant
LOC100506207	NR_038979.1	n.685-58155A>G		intron_variant
LOC100506207	NR_038980.1	n.707+93811A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000503668.2	n.254+64A>G		intron_variant		1
HULC	ENST00000646741.1	n.193A>G		non_coding_transcript_exon_variant	1/2
HULC	ENST00000665267.1	n.193A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66875 AN: 151954 Hom.: 15048 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.460

GnomAD4 exome AF: 0.375 AC: 30 AN: 80 Hom.: 6 Cov.: 0 AF XY: 0.375 AC XY: 24 AN XY: 64

Gnomad4 AFR exome AF: 0.167

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.440 AC: 66919 AN: 152070 Hom.: 15053 Cov.: 32 AF XY: 0.444 AC XY: 32987 AN XY: 74342

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.463

Alfa AF: 0.453 Hom.: 1949

Bravo AF: 0.432

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328867; hg19: chr6-8652687;