rs10493473

Variant names:

• chr1-70382532-A-G
• rs10493473
• ENST00000531950.1:n.460-2726A>G

Variant summary

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

The ENST00000531950.1(HHLA3):​n.460-2726A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,178 control chromosomes in the GnomAD database, including 2,316 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 0.17 (2316 hom., cov: 32)
• Consequence: HHLA3 ENST00000531950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

HHLA3 (HGNC:4906): (ANKRD13C divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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
HHLA3	ENST00000531950.1	n.460-2726A>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25757 AN: 152060 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.169 AC: 25768 AN: 152178 Hom.: 2316 Cov.: 32 AF XY: 0.167 AC XY: 12411 AN XY: 74396

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.177

Alfa AF: 0.179 Hom.: 402

Bravo AF: 0.167

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493473; hg19: chr1-70848215;