rs2184658

chr1-220879115-C-Gchr1-220879115-C-T

Variant summary

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

The ENST00000691443.1(ENSG00000289142):n.87G>C 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 0.203 in 152,226 control chromosomes in the GnomAD database, including 3,283 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 0.20 (3283 hom., cov: 33)
• Consequence: ENST00000691443.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

HLX-AS1 (HGNC:42509): (HLX antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLX-AS1	NR_046901.1	n.292+734G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691443.1	n.87G>C		non_coding_transcript_exon_variant	1/1
HLX-AS1	ENST00000552026.1	n.292+734G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30818 AN: 152108 Hom.: 3280 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.203 AC: 30834 AN: 152226 Hom.: 3283 Cov.: 33 AF XY: 0.201 AC XY: 14979 AN XY: 74416

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.175

Alfa AF: 0.112 Hom.: 181

Bravo AF: 0.195

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.71
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2184658; hg19: chr1-221052457;