19-9833901-A-T

Variant names:

• chr19-9833901-A-T
• rs7247933
• ENST00000591174.2:n.1062T>A

Variant summary

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

The ENST00000591174.2(PIN1-DT):​n.1062T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 152,172 control chromosomes in the GnomAD database, including 75,034 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 0.99 (75034 hom., cov: 30)
• Consequence: PIN1-DT ENST00000591174.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 1 publications found

Genes affected

PIN1-DT (HGNC:55303): (PIN1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIN1-DT	NR_183873.1	n.*178T>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIN1-DT	ENST00000591174.2	n.1062T>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
PIN1-DT	ENST00000731113.1	n.1017T>A		non_coding_transcript_exon_variant	Exon 2 of 2
PIN1-DT	ENST00000731112.1	n.311+620T>A		intron_variant	Intron 2 of 3
PIN1-DT	ENST00000731114.1	n.*178T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.993 AC: 150931 AN: 152054 Hom.: 74975 Cov.: 30

Gnomad AFR AF: 0.999

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.977

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.991

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

GnomAD4 genome AF: 0.993 AC: 151050 AN: 152172 Hom.: 75034 Cov.: 30 AF XY: 0.992 AC XY: 73788 AN XY: 74402

African (AFR) AF: 0.999 AC: 41459 AN: 41498

American (AMR) AF: 0.997 AC: 15228 AN: 15278

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4335 AN: 5152

South Asian (SAS) AF: 0.977 AC: 4709 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10607 AN: 10608

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67943 AN: 68026

Other (OTH) AF: 0.990 AC: 2091 AN: 2112

Alfa AF: 0.997 Hom.: 9396

Bravo AF: 0.992

Asia WGS AF: 0.938 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7247933; hg19: chr19-9944577;