14-31964652-C-T

Variant names:

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

Variant summary

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

The ENST00000611153.1(ENSG00000290393):​n.103C>T 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 0.526 in 185,538 control chromosomes in the GnomAD database, including 26,467 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 0.54 (22468 hom., cov: 31)
  • Exomes 𝑓: 0.48 (3999 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81544 AN: 151884 Hom.: 22447 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.477 AC: 15990 AN: 33536 Hom.: 3999 Cov.: 0 AF XY: 0.476 AC XY: 9066 AN XY: 19038

African (AFR) AF: 0.580 AC: 651 AN: 1122

American (AMR) AF: 0.406 AC: 1782 AN: 4394

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 201 AN: 372

East Asian (EAS) AF: 0.828 AC: 1908 AN: 2304

South Asian (SAS) AF: 0.555 AC: 1566 AN: 2820

European-Finnish (FIN) AF: 0.346 AC: 1494 AN: 4322

Middle Eastern (MID) AF: 0.673 AC: 762 AN: 1132

European-Non Finnish (NFE) AF: 0.449 AC: 7080 AN: 15764

Other (OTH) AF: 0.418 AC: 546 AN: 1306

GnomAD4 genome AF: 0.537 AC: 81613 AN: 152002 Hom.: 22468 Cov.: 31 AF XY: 0.533 AC XY: 39606 AN XY: 74290

African (AFR) AF: 0.598 AC: 24792 AN: 41464

American (AMR) AF: 0.528 AC: 8067 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3470

East Asian (EAS) AF: 0.848 AC: 4358 AN: 5140

South Asian (SAS) AF: 0.576 AC: 2775 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4111 AN: 10556

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33799 AN: 67950

Other (OTH) AF: 0.557 AC: 1174 AN: 2106

Alfa AF: 0.523 Hom.: 33103

Bravo AF: 0.547

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.85
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;