rs915071

Variant names:

• chr14-31964652-C-A
• rs915071
• ENST00000611153.1:n.103C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-31964652-C-A
• chr14-31964652-C-G
• chr14-31964652-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000611153.1(ENSG00000290393):​n.103C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290393 ENST00000611153.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 19 publications found

Genes affected

ENSG00000290393 (HGNC:):

ZFAND2AP2 (HGNC:56473): (ZFAND2A pseudogene 2)

LINC02313 (HGNC:53232): (long intergenic non-protein coding RNA 2313)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFAND2AP2		n.31964652C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290393	ENST00000611153.1	n.103C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ZFAND2AP2	ENST00000613699.1	n.93C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000296087	ENST00000736324.1	n.320G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 33862 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 19200

African (AFR) AF: 0.00 AC: 0 AN: 1134

American (AMR) AF: 0.00 AC: 0 AN: 4454

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 374

East Asian (EAS) AF: 0.00 AC: 0 AN: 2318

South Asian (SAS) AF: 0.00 AC: 0 AN: 2842

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4344

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1134

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 15932

Other (OTH) AF: 0.00 AC: 0 AN: 1330

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 33103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.86
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs915071; hg19: chr14-32433858;