rs567317913

Variant names:

• chr12-19130072-C-A
• rs567317913
• NM_001256470.2:c.111C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-19130072-C-A
• chr12-19130072-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4 BP7

The NM_001256470.2(PLEKHA5):​c.111C>A​(p.Thr37Thr) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. T37T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLEKHA5 NM_001256470.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 1 publications found

Genes affected

PLEKHA5 (HGNC:30036): (pleckstrin homology domain containing A5) Predicted to enable phosphatidylinositol phosphate binding activity. Predicted to act upstream of or within reproductive system development. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.14).
• BP7: Synonymous conserved (PhyloP=2.01 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256470.2. 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
	PLEKHA5	NM_001256470.2	MANE Select	c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 32	NP_001243399.1	Q9HAU0-6
	PLEKHA5	NM_001385923.1		c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 31	NP_001372852.1
	PLEKHA5	NM_001385924.1		c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 31	NP_001372853.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLEKHA5	ENST00000429027.7	TSL:1 MANE Select	c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 32	ENSP00000404296.2	Q9HAU0-6
	PLEKHA5	ENST00000538714.5	TSL:1	c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 28	ENSP00000439673.1	Q9HAU0-2
	PLEKHA5	ENST00000299275.10	TSL:1	c.111C>A	p.Thr37Thr	synonymous	Exon 2 of 26	ENSP00000299275.6	Q9HAU0-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD2 exomes AF: 0.00000475 AC: 1 AN: 210322 AF XY: 0.00000872

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000107

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1439250 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 714472

African (AFR) AF: 0.00 AC: 0 AN: 32074

American (AMR) AF: 0.00 AC: 0 AN: 42452

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25438

East Asian (EAS) AF: 0.00 AC: 0 AN: 38006

South Asian (SAS) AF: 0.00 AC: 0 AN: 82600

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51104

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5734

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1102352

Other (OTH) AF: 0.00 AC: 0 AN: 59490

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	17
DANN	Benign	0.97
PhyloP100		2.0
PromoterAI		0.11	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs567317913; hg19: chr12-19283006;