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 ENST00000736324.1(ENSG00000296087):​n.320G>T 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: ENSG00000296087 ENST00000736324.1 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736324.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290393	ENST00000611153.1	TSL:6	n.103C>A		non_coding_transcript_exon	Exon 1 of 1
	ZFAND2AP2	ENST00000613699.1	TSL:6	n.93C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000296087	ENST00000736324.1		n.320G>T		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs915071;

hg19: chr14-32433858;