rs3806325

Positions:

• chr1-220878450-C-T

Variant summary

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

The ENST00000691443.1(ENSG00000289142):​n.752G>A 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 0.137 in 152,194 control chromosomes in the GnomAD database, including 1,883 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 0.14 (1883 hom., cov: 32)
• Consequence: ENST00000691443.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLX-AS1	NR_046901.1	n.292+1399G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691443.1	n.752G>A		non_coding_transcript_exon_variant	1/1
HLX-AS1	ENST00000552026.1	n.292+1399G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20892 AN: 152076 Hom.: 1883 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.137 AC: 20891 AN: 152194 Hom.: 1883 Cov.: 32 AF XY: 0.137 AC XY: 10202 AN XY: 74396

Gnomad4 AFR AF: 0.0387

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.127

Alfa AF: 0.172 Hom.: 3095

Bravo AF: 0.122

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806325; hg19: chr1-221051792;