rs1131709

chr18-35307950-A-Gchr18-35307950-A-T

Variant summary

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

The NR_024565.1(ZNF271P):n.2318A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 512,812 control chromosomes in the GnomAD database, including 68,797 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 0.53 (21433 hom., cov: 32)
  • Exomes 𝑓: 0.51 (47364 hom.)
• Consequence: ZNF271P NR_024565.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

Genes affected

ZNF271P (HGNC:13065): (zinc finger protein 271, pseudogene) Zinc finger proteins interact with nucleic acids and have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF271P	NR_024565.1	n.2318A>G		non_coding_transcript_exon_variant	3/3
ZNF271P	NR_024566.1	n.2095A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF271P	ENST00000638208.3	n.2091A>G		non_coding_transcript_exon_variant	2/2	1
ZNF271P	ENST00000639248.1	n.2266A>G		non_coding_transcript_exon_variant	3/5	5
ZNF271P	ENST00000399070.3	n.2308A>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80353 AN: 151912 Hom.: 21434 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.548

GnomAD4 exome AF: 0.507 AC: 182937 AN: 360782 Hom.: 47364 Cov.: 0 AF XY: 0.510 AC XY: 104725 AN XY: 205416

Gnomad4 AFR exome AF: 0.557

Gnomad4 AMR exome AF: 0.414

Gnomad4 ASJ exome AF: 0.614

Gnomad4 EAS exome AF: 0.367

Gnomad4 SAS exome AF: 0.495

Gnomad4 FIN exome AF: 0.419

Gnomad4 NFE exome AF: 0.542

Gnomad4 OTH exome AF: 0.519

GnomAD4 genome AF: 0.529 AC: 80388 AN: 152030 Hom.: 21433 Cov.: 32 AF XY: 0.522 AC XY: 38787 AN XY: 74294

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.546

Alfa AF: 0.441 Hom.: 1986

Bravo AF: 0.536

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	9.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1131709; hg19: chr18-32887914; COSMIC: COSV67580879;