rs16942887

Variant names:

• chr16-67894139-G-A
• rs16942887
• NM_006742.3:c.-71+768G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 114 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PSKH1	NM_006742.3	c.-71+768G>A		intron_variant	Intron 1 of 2	ENST00000291041.6	NP_006733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSKH1	ENST00000291041.6	c.-71+768G>A		intron_variant	Intron 1 of 2	1	NM_006742.3	ENSP00000291041.4
PSKH1	ENST00000570631.5	c.-71+768G>A		intron_variant	Intron 1 of 1	1		ENSP00000482880.1
PSKH1	ENST00000575198.1	n.71+768G>A		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.217 AC: 9009 AN: 41488

American (AMR) AF: 0.144 AC: 2201 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5186

South Asian (SAS) AF: 0.184 AC: 885 AN: 4816

European-Finnish (FIN) AF: 0.163 AC: 1725 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8403 AN: 68000

Other (OTH) AF: 0.141 AC: 297 AN: 2110

Alfa AF: 0.131 Hom.: 5994

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
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16942887; hg19: chr16-67928042;