chr11-117168609-T-C

Variant names:

• chr11-117168609-T-C
• rs10892082
• NM_002572.4:c.*910T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002572.4(PAFAH1B2):​c.*910T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 26)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PAFAH1B2 NM_002572.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961
• Publications: 11 publications found

Genes affected

PAFAH1B2 (HGNC:8575): (platelet activating factor acetylhydrolase 1b catalytic subunit 2) Platelet-activating factor acetylhydrolase (PAFAH) inactivates platelet-activating factor (PAF) into acetate and LYSO-PAF. This gene encodes the beta subunit of PAFAH, the other subunits are alpha and gamma. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jan 2014]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002572.4. 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
	PAFAH1B2	NM_002572.4	MANE Select	c.*910T>C		3_prime_UTR	Exon 6 of 6	NP_002563.1
	PAFAH1B2	NR_110282.2		n.1444T>C		non_coding_transcript_exon	Exon 3 of 3
	PAFAH1B2	NM_001309431.2		c.*910T>C		3_prime_UTR	Exon 5 of 5	NP_001296360.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAFAH1B2	ENST00000527958.6	TSL:1 MANE Select	c.*910T>C		3_prime_UTR	Exon 6 of 6	ENSP00000435289.1
	PAFAH1B2	ENST00000530272.1	TSL:1	c.412-3013T>C		intron	N/A	ENSP00000431365.1
	PAFAH1B2	ENST00000529887.6	TSL:1	c.411+4717T>C		intron	N/A	ENSP00000434951.2

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 911784 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 420918

African (AFR) AF: 0.00 AC: 0 AN: 19576

American (AMR) AF: 0.00 AC: 0 AN: 3410

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10138

East Asian (EAS) AF: 0.00 AC: 0 AN: 14776

South Asian (SAS) AF: 0.00 AC: 0 AN: 17138

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 332

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2096

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 810444

Other (OTH) AF: 0.00 AC: 0 AN: 33874

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs10892082; hg19: chr11-117039325;