chr1-204350779-C-T

Position:

• chr1-204350779-C-T

Variant summary

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

The NM_014935.5(PLEKHA6):​c.-95+8915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,010 control chromosomes in the GnomAD database, including 36,622 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 0.69 (36622 hom., cov: 32)
• Consequence: PLEKHA6 NM_014935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

PLEKHA6 (HGNC:17053): (pleckstrin homology domain containing A6)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLEKHA6	NM_014935.5	c.-95+8915G>A		intron_variant		ENST00000272203.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLEKHA6	ENST00000272203.8	c.-95+8915G>A		intron_variant		1	NM_014935.5	P2
PLEKHA6	ENST00000414478.1	c.-95+8915G>A		intron_variant		5
PLEKHA6	ENST00000564627.2	c.218+17020G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105080 AN: 151892 Hom.: 36591 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.692 AC: 105165 AN: 152010 Hom.: 36622 Cov.: 32 AF XY: 0.693 AC XY: 51521 AN XY: 74304

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.714

Alfa AF: 0.683 Hom.: 4424

Bravo AF: 0.703

Asia WGS AF: 0.728 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.70

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: rs7513240; hg19: chr1-204319907;