rs1656966

Positions:

• chr3-186748463-G-A
• chr3-186748463-G-C
• chr3-186748463-G-T

Variant summary

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

The ENST00000596329.3(HRG-AS1):​n.515-1643C>T 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 0.18 in 151,992 control chromosomes in the GnomAD database, including 2,550 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 0.18 (2550 hom., cov: 31)
• Consequence: HRG-AS1 ENST00000596329.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

HRG-AS1 (HGNC:55915): (HRG and FETUB antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HRG-AS1	ENST00000596329.3	n.515-1643C>T		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000596632.1	n.432-3261C>T		intron_variant, non_coding_transcript_variant		5
HRG-AS1	ENST00000599314.5	n.61-4622C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27287 AN: 151874 Hom.: 2552 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.180 AC: 27300 AN: 151992 Hom.: 2550 Cov.: 31 AF XY: 0.181 AC XY: 13461 AN XY: 74298

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.151

Alfa AF: 0.168 Hom.: 4370

Bravo AF: 0.176

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1656966; hg19: chr3-186466252;