19-9834111-G-C

Variant names:

• chr19-9834111-G-C
• rs4804459
• ENST00000591174.2:n.852C>G

Variant summary

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

The ENST00000591174.2(PIN1-DT):​n.852C>G 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 0.801 in 152,114 control chromosomes in the GnomAD database, including 49,627 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 0.80 (49624 hom., cov: 31)
  • Exomes 𝑓: 0.67 (3 hom.)
• Consequence: PIN1-DT ENST00000591174.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591174.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIN1-DT	NR_183873.1		n.720C>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIN1-DT	ENST00000591174.2	TSL:3	n.852C>G		non_coding_transcript_exon	Exon 2 of 2
	PIN1-DT	ENST00000731113.1		n.807C>G		non_coding_transcript_exon	Exon 2 of 2
	PIN1-DT	ENST00000731114.1		n.815C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121798 AN: 151984 Hom.: 49592 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 0.667 AC: 8 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.801 AC: 121890 AN: 152102 Hom.: 49624 Cov.: 31 AF XY: 0.796 AC XY: 59201 AN XY: 74338

African (AFR) AF: 0.914 AC: 37922 AN: 41502

American (AMR) AF: 0.834 AC: 12736 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2853 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2351 AN: 5162

South Asian (SAS) AF: 0.642 AC: 3097 AN: 4826

European-Finnish (FIN) AF: 0.715 AC: 7557 AN: 10564

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52842 AN: 68000

Other (OTH) AF: 0.812 AC: 1711 AN: 2106

Alfa AF: 0.738 Hom.: 2181

Bravo AF: 0.815

Asia WGS AF: 0.591 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.0
DANN	Benign	0.74
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs4804459; hg19: chr19-9944787;