rs17564097

Positions:

• chr10-122435300-A-G

Variant summary

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

The NM_021622.5(PLEKHA1):​c.*5362A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,272 control chromosomes in the GnomAD database, including 1,340 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 0.11 (1340 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: PLEKHA1 NM_021622.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

PLEKHA1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEKHA1	NM_001195608.2	c.*5717A>G		3_prime_UTR_variant	14/14		NP_001182537.1
PLEKHA1	NM_001330178.2	c.*5466A>G		3_prime_UTR_variant	14/14		NP_001317107.1
PLEKHA1	NM_001377230.1	c.*5362A>G		3_prime_UTR_variant	13/13		NP_001364159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17132 AN: 152154 Hom.: 1341 Cov.: 31

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.129

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.112 AC: 17127 AN: 152272 Hom.: 1340 Cov.: 31 AF XY: 0.110 AC XY: 8203 AN XY: 74456

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.127

Alfa AF: 0.139 Hom.: 226

Bravo AF: 0.103

Asia WGS AF: 0.0170 AC: 61 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.78

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: rs17564097; hg19: chr10-124194816;