rs10518262

chr19-43130018-T-A

Variant summary

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

The ENST00000635495.1(PSG11-AS1):n.322+28318T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 151,518 control chromosomes in the GnomAD database, including 916 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 0.096 (916 hom., cov: 31)
• Consequence: PSG11-AS1 ENST00000635495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

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 (AMR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSG11-AS1	ENST00000635495.1	n.322+28318T>A		intron_variant, non_coding_transcript_variant		5
PSG11-AS1	ENST00000635346.1	n.141-7499T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14485 AN: 151400 Hom.: 918 Cov.: 31

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.0955 AC: 14477 AN: 151518 Hom.: 916 Cov.: 31 AF XY: 0.0953 AC XY: 7060 AN XY: 74076

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00426

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0983

Alfa AF: 0.107 Hom.: 132

Bravo AF: 0.0993

Asia WGS AF: 0.0930 AC: 323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518262; hg19: chr19-43634170;