3-186715310-T-C

Variant names:

• chr3-186715310-T-C
• rs11924390
• ENST00000354642.4:n.651-771A>G

Variant summary

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

The ENST00000354642.4(HRG-AS1):​n.651-771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,664 control chromosomes in the GnomAD database, including 10,032 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 0.36 (10032 hom., cov: 30)
• Consequence: HRG-AS1 ENST00000354642.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 28 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000354642.4. 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	ENST00000354642.4	TSL:5	n.651-771A>G		intron	N/A
	HRG-AS1	ENST00000625303.2	TSL:5	n.214+3157A>G		intron	N/A
	HRG-AS1	ENST00000625386.2	TSL:5	n.213+3157A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53886 AN: 151544 Hom.: 10022 Cov.: 30

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.356 AC: 53938 AN: 151664 Hom.: 10032 Cov.: 30 AF XY: 0.353 AC XY: 26135 AN XY: 74136

African (AFR) AF: 0.458 AC: 18919 AN: 41290

American (AMR) AF: 0.286 AC: 4368 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1641 AN: 5128

South Asian (SAS) AF: 0.432 AC: 2081 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3207 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21596 AN: 67854

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.325 Hom.: 20163

Bravo AF: 0.355

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.36
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11924390;

hg19: chr3-186433099;

COSMIC: COSV107286310;