chr3-186748463-G-A

Variant names:

• chr3-186748463-G-A
• rs1656966
• ENST00000596329.3:n.515-1643C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000596329.3(HRG-AS1):​n.515-1643C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000596329.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HRG-AS1	ENST00000596329.3	TSL:5	n.515-1643C>T		intron	N/A
	HRG-AS1	ENST00000596632.1	TSL:5	n.432-3261C>T		intron	N/A
	HRG-AS1	ENST00000599314.5	TSL:5	n.61-4622C>T		intron	N/A

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

African (AFR) AF: 0.200 AC: 8311 AN: 41470

American (AMR) AF: 0.138 AC: 2094 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3462

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5164

South Asian (SAS) AF: 0.149 AC: 719 AN: 4822

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10562

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11769 AN: 67978

Other (OTH) AF: 0.151 AC: 319 AN: 2112

Alfa AF: 0.174 Hom.: 9963

Bravo AF: 0.176

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1656966; hg19: chr3-186466252;