10-122442149-T-G

Position:

• chr10-122442149-T-G

Variant summary

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

The ENST00000650300.1(ENSG00000285955):​n.1853-5517A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,280 control chromosomes in the GnomAD database, including 1,498 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 0.12 (1496 hom., cov: 32)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: ENST00000650300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEKHA1	NM_001195608.2	c.*12566T>G		3_prime_UTR_variant	14/14		NP_001182537.1
PLEKHA1	NM_001330178.2	c.*12315T>G		3_prime_UTR_variant	14/14		NP_001317107.1
PLEKHA1	NM_001377230.1	c.*12211T>G		3_prime_UTR_variant	13/13		NP_001364159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650300.1	n.1853-5517A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17603 AN: 152120 Hom.: 1491 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.190 AC: 8 AN: 42 Hom.: 2 Cov.: 0 AF XY: 0.184 AC XY: 7 AN XY: 38

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.116 AC: 17616 AN: 152238 Hom.: 1496 Cov.: 32 AF XY: 0.121 AC XY: 9026 AN XY: 74420

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.116

Alfa AF: 0.123 Hom.: 1754

Bravo AF: 0.112

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.42

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: rs2292627; hg19: chr10-124201665;