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

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>T		non_coding_transcript_exon	Exon 1 of 1
	ZFAND2AP2	ENST00000613699.1	TSL:6	n.93C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000296087	ENST00000736324.1		n.320G>A		non_coding_transcript_exon	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 v4.9

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

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;