rs1131709

Variant names:

• chr18-35307950-A-G
• rs1131709
• ENST00000638208.4:n.2099A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-35307950-A-G
• chr18-35307950-A-T

Variant summary

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

The ENST00000638208.4(ZNF271P):​n.2099A>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 ENST00000638208.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 16 publications found

Genes affected

ZNF271P (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638208.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF271P	NR_024565.1		n.2318A>G		non_coding_transcript_exon	Exon 3 of 3
	ZNF271P	NR_024566.1		n.2095A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF271P	ENST00000638208.4	TSL:1	n.2099A>G		non_coding_transcript_exon	Exon 2 of 2
	ZNF271P	ENST00000399070.4	TSL:2	n.2316A>G		non_coding_transcript_exon	Exon 3 of 3
	ZNF271P	ENST00000639248.1	TSL:5	n.2266A>G		non_coding_transcript_exon	Exon 3 of 5

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

African (AFR) AF: 0.557 AC: 5577 AN: 10016

American (AMR) AF: 0.414 AC: 13924 AN: 33646

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 6730 AN: 10958

East Asian (EAS) AF: 0.367 AC: 4591 AN: 12510

South Asian (SAS) AF: 0.495 AC: 31752 AN: 64086

European-Finnish (FIN) AF: 0.419 AC: 13027 AN: 31088

Middle Eastern (MID) AF: 0.564 AC: 1568 AN: 2780

European-Non Finnish (NFE) AF: 0.542 AC: 97585 AN: 179922

Other (OTH) AF: 0.519 AC: 8183 AN: 15776

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

African (AFR) AF: 0.557 AC: 23078 AN: 41466

American (AMR) AF: 0.498 AC: 7609 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1986 AN: 5168

South Asian (SAS) AF: 0.492 AC: 2371 AN: 4818

European-Finnish (FIN) AF: 0.416 AC: 4388 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37106 AN: 67974

Other (OTH) AF: 0.546 AC: 1152 AN: 2108

Alfa AF: 0.499 Hom.: 6289

Bravo AF: 0.536

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.4
DANN	Benign	0.78
PhyloP100		1.7

Splicing

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

Other links and lift over

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