16-67894139-G-A

Position:

• chr16-67894139-G-A

Variant summary

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

The NM_006742.3(PSKH1):​c.-71+768G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,146 control chromosomes in the GnomAD database, including 1,958 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 0.15 (1958 hom., cov: 32)
• Consequence: PSKH1 NM_006742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

Genes affected

PSKH1 (HGNC:9529): (protein serine kinase H1) Predicted to enable protein kinase activity. Predicted to act upstream of or within determination of left/right symmetry; heart development; and protein phosphorylation. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

PSKH1 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSKH1	NM_006742.3	c.-71+768G>A		intron_variant		ENST00000291041.6	NP_006733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSKH1	ENST00000291041.6	c.-71+768G>A		intron_variant		1	NM_006742.3	ENSP00000291041.4
PSKH1	ENST00000570631.5	c.-71+768G>A		intron_variant		1		ENSP00000482880.1
PSKH1	ENST00000575198.1	n.71+768G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23200 AN: 152028 Hom.: 1959 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.153 AC: 23205 AN: 152146 Hom.: 1958 Cov.: 32 AF XY: 0.154 AC XY: 11485 AN XY: 74372

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.141

Alfa AF: 0.127 Hom.: 2479

Bravo AF: 0.152

Asia WGS AF: 0.154 AC: 537 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	4.7
DANN	Benign	0.80

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: rs16942887; hg19: chr16-67928042;