11-69639561-ACC-AC

Variant names:

• chr11-69639561-AC-A
• rs36225395
• ENST00000754571.1:n.435delC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000754571.1(PNCRNA-D):​n.435delC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (22287 hom., cov: 0)
• Consequence: PNCRNA-D ENST00000754571.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 2 publications found

Genes affected

PNCRNA-D (HGNC:58269):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754571.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNCRNA-D	ENST00000754571.1		n.435delC		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 79801 AN: 140620 Hom.: 22254 Cov.: 0

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.568 AC: 79867 AN: 140702 Hom.: 22287 Cov.: 0 AF XY: 0.576 AC XY: 39056 AN XY: 67794

African (AFR) AF: 0.615 AC: 23041 AN: 37456

American (AMR) AF: 0.540 AC: 7280 AN: 13470

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 1963 AN: 3398

East Asian (EAS) AF: 0.841 AC: 3957 AN: 4704

South Asian (SAS) AF: 0.715 AC: 3170 AN: 4434

European-Finnish (FIN) AF: 0.513 AC: 4301 AN: 8384

Middle Eastern (MID) AF: 0.579 AC: 162 AN: 280

European-Non Finnish (NFE) AF: 0.523 AC: 34413 AN: 65758

Other (OTH) AF: 0.605 AC: 1170 AN: 1934

Alfa AF: 0.316 Hom.: 558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.95

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs36225395;

hg19: chr11-69454329;