rs1150668

Variant names:

• chr6-28162011-T-G
• rs1150668
• ENST00000440790.6:c.-399+190T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440790.6(ZKSCAN8P1):​c.-399+190T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,910 control chromosomes in the GnomAD database, including 27,987 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 0.57 (27987 hom., cov: 30)
• Consequence: ZKSCAN8P1 ENST00000440790.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 26 publications found

Genes affected

ZKSCAN8P1 (HGNC:18777): (ZKSCAN8 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN8P1	NR_103448.1	n.61+190T>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZKSCAN8P1	ENST00000440790.6	c.-399+190T>G		intron_variant	Intron 1 of 4	5		ENSP00000509393.1
ZKSCAN8P1	ENST00000562227.2	c.-528+190T>G		intron_variant	Intron 1 of 5	3		ENSP00000510811.1
ZKSCAN8P1	ENST00000570126.1	n.30+190T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86616 AN: 151794 Hom.: 27922 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.571 AC: 86744 AN: 151910 Hom.: 27987 Cov.: 30 AF XY: 0.570 AC XY: 42332 AN XY: 74238

African (AFR) AF: 0.889 AC: 36871 AN: 41456

American (AMR) AF: 0.514 AC: 7845 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3468

East Asian (EAS) AF: 0.568 AC: 2915 AN: 5130

South Asian (SAS) AF: 0.545 AC: 2620 AN: 4810

European-Finnish (FIN) AF: 0.493 AC: 5204 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27911 AN: 67914

Other (OTH) AF: 0.559 AC: 1178 AN: 2106

Alfa AF: 0.544 Hom.: 13872

Bravo AF: 0.591

Asia WGS AF: 0.556 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.34
DANN	Benign	0.58
PhyloP100		-1.9
PromoterAI		0.27	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1150668; hg19: chr6-28129789;