rs1427828

Variant names:

• chr12-89368722-C-G
• rs1427828
• NM_001425794.1:c.1114-19161G>C

Variant summary

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

The NM_001425794.1(POC1B-DUSP6):​c.1114-19161G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,048 control chromosomes in the GnomAD database, including 17,902 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 0.47 (17890 hom., cov: 32)
  • Exomes 𝑓: 0.71 (12 hom.)
• Consequence: POC1B-DUSP6 NM_001425794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 8 publications found

Genes affected

POC1B-DUSP6 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001425794.1. 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
	POC1B-DUSP6	NM_001425794.1		c.1114-19161G>C		intron	N/A	NP_001412723.1
	POC1B-DUSP6	NM_001425795.1		c.1033-19161G>C		intron	N/A	NP_001412724.1
	POC1B-DUSP6	NM_001425796.1		c.643-19161G>C		intron	N/A	NP_001412725.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271327	ENST00000605595.1	TSL:6	n.916C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000286608	ENST00000657284.1		n.123+14802C>G		intron	N/A
	ENSG00000286608	ENST00000715377.2		n.222-1910C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71230 AN: 151894 Hom.: 17891 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.711 AC: 27 AN: 38 Hom.: 12 Cov.: 0 AF XY: 0.731 AC XY: 19 AN XY: 26

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 18 AN: 24

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.469 AC: 71248 AN: 152010 Hom.: 17890 Cov.: 32 AF XY: 0.475 AC XY: 35307 AN XY: 74294

African (AFR) AF: 0.278 AC: 11525 AN: 41448

American (AMR) AF: 0.490 AC: 7495 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1788 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3124 AN: 5156

South Asian (SAS) AF: 0.507 AC: 2442 AN: 4820

European-Finnish (FIN) AF: 0.630 AC: 6656 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36551 AN: 67954

Other (OTH) AF: 0.483 AC: 1022 AN: 2114

Alfa AF: 0.487 Hom.: 2341

Bravo AF: 0.453

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1427828; hg19: chr12-89762499;