ENST00000519951.2:c.1188-3315G>T

Variant names:

• chr8-43338564-G-T
• rs10504052
• ENST00000519951.2:c.1188-3315G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000519951.2(POTEA):​c.1188-3315G>T variant causes a intron 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: 33)
• Consequence: POTEA ENST00000519951.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 1 publications found

Genes affected

POTEA (HGNC:33893): (POTE ankyrin domain family member A)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POTEA	NM_001005365.2	c.1188-3315G>T		intron_variant	Intron 9 of 13		NP_001005365.2
POTEA	NM_001002920.1	c.1050-3315G>T		intron_variant	Intron 8 of 12		NP_001002920.1
POTEA	XM_024447146.1	c.1187+19942G>T		intron_variant	Intron 9 of 10		XP_024302914.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POTEA	ENST00000519951.2	c.1188-3315G>T		intron_variant	Intron 9 of 13	1		ENSP00000492193.1
POTEA	ENST00000522175.7	c.1050-3315G>T		intron_variant	Intron 8 of 12	1		ENSP00000492265.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 9

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.35
DANN	Benign	0.69
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10504052; hg19: chr8-43193707;