rs10402173

Variant names:

• chr19-43133064-G-A
• rs10402173
• ENST00000635346.1:n.141-4453G>A

Variant summary

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

The ENST00000635346.1(PSG11-AS1):​n.141-4453G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,498 control chromosomes in the GnomAD database, including 3,086 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 (3086 hom., cov: 31)
• Consequence: PSG11-AS1 ENST00000635346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

PSG11-AS1 (HGNC:56358): (PSG11, PSG2 and PSG5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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
PSG11-AS1	ENST00000635346.1	n.141-4453G>A		intron_variant	Intron 1 of 1	3
PSG11-AS1	ENST00000635495.1	n.322+31364G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28900 AN: 151380 Hom.: 3089 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.191 AC: 28905 AN: 151498 Hom.: 3086 Cov.: 31 AF XY: 0.190 AC XY: 14094 AN XY: 74050

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.181

Alfa AF: 0.192 Hom.: 523

Bravo AF: 0.194

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10402173; hg19: chr19-43637216;