chr14-31964652-C-T

Position:

• chr14-31964652-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000290393 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZFAND2AP2		n.31964652C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290393	ENST00000611153.1	n.103C>T		non_coding_transcript_exon_variant	1/1	6
ZFAND2AP2	ENST00000613699.1	n.93C>T		non_coding_transcript_exon_variant	1/1	6

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

Gnomad4 AFR exome AF: 0.580

Gnomad4 AMR exome AF: 0.406

Gnomad4 ASJ exome AF: 0.540

Gnomad4 EAS exome AF: 0.828

Gnomad4 SAS exome AF: 0.555

Gnomad4 FIN exome AF: 0.346

Gnomad4 NFE exome AF: 0.449

Gnomad4 OTH exome AF: 0.418

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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.557

Alfa AF: 0.516 Hom.: 15908

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs915071; hg19: chr14-32433858;