rs7195303

chr16-75133681-G-Achr16-75133681-G-Cchr16-75133681-G-T

Variant summary

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

The ENST00000563098.1(ENSG00000261058):n.397+1059G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,308 control chromosomes in the GnomAD database, including 64,486 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 0.92 (64486 hom., cov: 33)
• Consequence: ENST00000563098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFP1	XM_011522921.3	c.35+1059G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563098.1	n.397+1059G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139886 AN: 152190 Hom.: 64425 Cov.: 33

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.919 AC: 140004 AN: 152308 Hom.: 64486 Cov.: 33 AF XY: 0.918 AC XY: 68350 AN XY: 74474

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.906

Alfa AF: 0.917 Hom.: 32699

Bravo AF: 0.920

Asia WGS AF: 0.831 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7195303; hg19: chr16-75167579;