6-28162011-T-G

Position:

• chr6-28162011-T-G

Variant summary

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

The ENST00000562227.2(ZKSCAN8P1):​c.-528+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 ENST00000562227.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZKSCAN8P1	NR_103448.1	n.61+190T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZKSCAN8P1	ENST00000562227.2	c.-528+190T>G		intron_variant		3		P1
ZKSCAN8P1	ENST00000440790.6	c.-399+190T>G		intron_variant		5		P1
ZKSCAN8P1	ENST00000570126.1	n.30+190T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.559

Alfa AF: 0.476 Hom.: 6761

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150668; hg19: chr6-28129789;