rs6983267

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000645438.1(POU5F1B):​c.-559-13828G>T variant causes a intron change. The variant allele was found at a frequency of 0.382 in 152,144 control chromosomes in the GnomAD database, including 13,516 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 0.38 ( 13516 hom., cov: 33)
Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

POU5F1B
ENST00000645438.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38
Variant links:
Genes affected
POU5F1B (HGNC:9223): (POU class 5 homeobox 1B) This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development. [provided by RefSeq, Apr 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCAT2NR_109834.1 linkuse as main transcriptn.662G>T non_coding_transcript_exon_variant 1/1
CASC8NR_117100.1 linkuse as main transcriptn.1176+19769C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CASC8ENST00000501396.5 linkuse as main transcriptn.546+19769C>A intron_variant 1
CASC8ENST00000502082.5 linkuse as main transcriptn.1176+19769C>A intron_variant 1
CASC8ENST00000523825.2 linkuse as main transcriptn.546+19769C>A intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.382
AC:
58042
AN:
152022
Hom.:
13511
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.506
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.495
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.491
Gnomad OTH
AF:
0.418
GnomAD4 exome
AF:
0.250
AC:
1
AN:
4
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.382
AC:
58042
AN:
152140
Hom.:
13516
Cov.:
33
AF XY:
0.386
AC XY:
28736
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.442
Gnomad4 ASJ
AF:
0.506
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.495
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.491
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.475
Hom.:
40970
Bravo
AF:
0.364
Asia WGS
AF:
0.503
AC:
1750
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
18
DANN
Benign
0.86

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6983267; hg19: chr8-128413305; COSMIC: COSV72370033; COSMIC: COSV72370033; API