rs10423723

Variant names:

• chr19-35106716-C-T
• rs10423723
• ENST00000648240.1:c.-393C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648240.1(ENSG00000285526):​c.-393C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 455,978 control chromosomes in the GnomAD database, including 46,116 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 0.48 (17878 hom., cov: 32)
  • Exomes 𝑓: 0.43 (28238 hom.)
• Consequence: ENSG00000285526 ENST00000648240.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 6 publications found

Genes affected

ENSG00000285526 (HGNC:):

HPN-AS1 (HGNC:47041): (HPN antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.021).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648240.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285526	ENST00000648240.1		c.-393C>T		5_prime_UTR	Exon 1 of 9	ENSP00000497169.1
	ENSG00000179066	ENST00000313865.6	TSL:6	n.748C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000179066	ENST00000616460.2	TSL:6	n.748C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72274 AN: 151884 Hom.: 17861 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.459

GnomAD2 exomes AF: 0.431 AC: 55349 AN: 128418 AF XY: 0.427

Gnomad AFR exome AF: 0.604

Gnomad AMR exome AF: 0.429

Gnomad ASJ exome AF: 0.448

Gnomad EAS exome AF: 0.451

Gnomad FIN exome AF: 0.379

Gnomad NFE exome AF: 0.427

Gnomad OTH exome AF: 0.414

GnomAD4 exome AF: 0.428 AC: 130124 AN: 303976 Hom.: 28238 Cov.: 0 AF XY: 0.424 AC XY: 73369 AN XY: 173082

African (AFR) AF: 0.604 AC: 5214 AN: 8628

American (AMR) AF: 0.428 AC: 11679 AN: 27282

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 4768 AN: 10790

East Asian (EAS) AF: 0.440 AC: 4051 AN: 9210

South Asian (SAS) AF: 0.405 AC: 24203 AN: 59744

European-Finnish (FIN) AF: 0.382 AC: 4724 AN: 12366

Middle Eastern (MID) AF: 0.420 AC: 1169 AN: 2782

European-Non Finnish (NFE) AF: 0.428 AC: 68027 AN: 158942

Other (OTH) AF: 0.442 AC: 6289 AN: 14232

GnomAD4 genome AF: 0.476 AC: 72327 AN: 152002 Hom.: 17878 Cov.: 32 AF XY: 0.473 AC XY: 35165 AN XY: 74302

African (AFR) AF: 0.608 AC: 25184 AN: 41432

American (AMR) AF: 0.452 AC: 6905 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2314 AN: 5174

South Asian (SAS) AF: 0.408 AC: 1972 AN: 4830

European-Finnish (FIN) AF: 0.373 AC: 3932 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29153 AN: 67958

Other (OTH) AF: 0.455 AC: 961 AN: 2112

Alfa AF: 0.444 Hom.: 24888

Bravo AF: 0.484

Asia WGS AF: 0.427 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.3
DANN	Benign	0.94
PhyloP100		-1.2
PromoterAI		0.0040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10423723; hg19: chr19-35597620; COSMIC: COSV107381178;