chr19-43130018-T-A

Variant names:

• chr19-43130018-T-A
• rs10518262
• ENST00000635346.1:n.141-7499T>A

Variant summary

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

The ENST00000635346.1(PSG11-AS1):​n.141-7499T>A variant causes a intron 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 ENST00000635346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 1 publications found

Genes affected

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

ENSG00000307623 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSG11-AS1	ENST00000635346.1	n.141-7499T>A		intron_variant	Intron 1 of 1	3
PSG11-AS1	ENST00000635495.1	n.322+28318T>A		intron_variant	Intron 2 of 2	5
ENSG00000307623	ENST00000827522.1	n.165-4347A>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0506 AC: 2076 AN: 41038

American (AMR) AF: 0.147 AC: 2231 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 400 AN: 3462

East Asian (EAS) AF: 0.00426 AC: 22 AN: 5170

South Asian (SAS) AF: 0.142 AC: 681 AN: 4806

European-Finnish (FIN) AF: 0.0790 AC: 836 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7902 AN: 67944

Other (OTH) AF: 0.0983 AC: 207 AN: 2106

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
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs10518262; hg19: chr19-43634170;