chr11-111283347-A-C

Position:

• chr11-111283347-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198498.3(POU2AF2):​c.164-729A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,886 control chromosomes in the GnomAD database, including 38,004 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 0.71 (38004 hom., cov: 30)
• Consequence: POU2AF2 NM_198498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

Genes affected

POU2AF2 (HGNC:30527): (POU class 2 homeobox associating factor 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2AF2	NM_198498.3	c.164-729A>C		intron_variant		ENST00000280325.7
POU2AF2	XM_011542804.3	c.98-729A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2AF2	ENST00000280325.7	c.164-729A>C		intron_variant		5	NM_198498.3	P1
POU2AF2	ENST00000637637.1	c.8-729A>C		intron_variant		1
POU2AF2	ENST00000635886.1	c.121-729A>C		intron_variant, NMD_transcript_variant		5
POU2AF2	ENST00000667535.1	n.154-729A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107129 AN: 151768 Hom.: 37965 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.706 AC: 107223 AN: 151886 Hom.: 38004 Cov.: 30 AF XY: 0.711 AC XY: 52726 AN XY: 74206

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.715

Alfa AF: 0.678 Hom.: 7015

Bravo AF: 0.699

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7130173; hg19: chr11-111154072;