chr6-9139420-T-C

Position:

• chr6-9139420-T-C

Variant summary

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

The ENST00000431369.1(ENSG00000225775):​n.175+1601A>G 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 0.568 in 152,120 control chromosomes in the GnomAD database, including 27,946 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 0.57 (27946 hom., cov: 33)
• Consequence: ENST00000431369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

Genes affected

(HGNC:):

HULC (HGNC:34232): (hepatocellular carcinoma up-regulated long non-coding RNA) This gene produces a long RNA that was discovered as upregulated in hepatocellular carcinoma and is associated with cancer progression. Expression of this transcript is regulated by microRNAs and at the transcriptional level by Sp1 family factors. The transcript may regulate gene expression by functioning as a competing RNA for microRNAs. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986562	XR_001743957.2	n.76+903A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431369.1	n.175+1601A>G		intron_variant, non_coding_transcript_variant		2
HULC	ENST00000645747.1	n.579+92929T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86323 AN: 152002 Hom.: 27945 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.568 AC: 86331 AN: 152120 Hom.: 27946 Cov.: 33 AF XY: 0.559 AC XY: 41563 AN XY: 74360

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.581

Alfa AF: 0.706 Hom.: 78125

Bravo AF: 0.541

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs767022; hg19: chr6-9139653;