rs6787344

Variant names:

• chr3-186622052-G-C
• rs6787344
• ENST00000625386.2:n.388+19902C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-186622052-G-C
• chr3-186622052-G-T

Variant summary

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

The ENST00000625386.2(HRG-AS1):​n.388+19902C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,056 control chromosomes in the GnomAD database, including 3,429 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 0.19 (3429 hom., cov: 32)
• Consequence: HRG-AS1 ENST00000625386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HRG-AS1	ENST00000625386.2	n.388+19902C>G		intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000628505.2	n.390-15743C>G		intron_variant	Intron 3 of 3	5
HRG-AS1	ENST00000630178.2	n.239-42086C>G		intron_variant	Intron 2 of 2	5
HRG-AS1	ENST00000840331.1	n.174+13467C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28164 AN: 151938 Hom.: 3425 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.185 AC: 28176 AN: 152056 Hom.: 3429 Cov.: 32 AF XY: 0.182 AC XY: 13572 AN XY: 74368

African (AFR) AF: 0.342 AC: 14153 AN: 41420

American (AMR) AF: 0.152 AC: 2332 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3472

East Asian (EAS) AF: 0.122 AC: 634 AN: 5184

South Asian (SAS) AF: 0.199 AC: 958 AN: 4812

European-Finnish (FIN) AF: 0.0914 AC: 968 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7952 AN: 67976

Other (OTH) AF: 0.192 AC: 404 AN: 2108

Alfa AF: 0.137 Hom.: 257

Bravo AF: 0.196

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6787344; hg19: chr3-186339841;