rs354033

Positions:

• chr7-149592373-G-A

Variant summary

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

The NR_027788.1(ZNF767P):​n.663+27551C>T 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 0.241 in 151,976 control chromosomes in the GnomAD database, including 4,557 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 0.24 (4557 hom., cov: 32)
• Consequence: ZNF767P NR_027788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

Genes affected

ZNF767P (HGNC:21884): (zinc finger family member 767, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF767P	NR_027788.1	n.663+27551C>T		intron_variant, non_coding_transcript_variant
ZNF767P	NR_027789.1	n.790+27551C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF767P	ENST00000472212.5	n.752+27551C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36552 AN: 151858 Hom.: 4558 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.241 AC: 36554 AN: 151976 Hom.: 4557 Cov.: 32 AF XY: 0.235 AC XY: 17419 AN XY: 74268

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.258

Alfa AF: 0.254 Hom.: 7255

Bravo AF: 0.240

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs354033; hg19: chr7-149289464;