14-103716661-C-T

Position:

• chr14-103716661-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024071.4(ZFYVE21):​c.138+682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,214 control chromosomes in the GnomAD database, including 2,760 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 0.18 (2760 hom., cov: 33)
• Consequence: ZFYVE21 NM_024071.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

ZFYVE21 (HGNC:20760): (zinc finger FYVE-type containing 21) Predicted to enable metal ion binding activity. Predicted to be located in endosome and focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ZFYVE21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFYVE21	NM_024071.4	c.138+682C>T		intron_variant		ENST00000311141.7	NP_076976.1
ZFYVE21	NM_001198953.2	c.138+682C>T		intron_variant			NP_001185882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFYVE21	ENST00000311141.7	c.138+682C>T		intron_variant		1	NM_024071.4	ENSP00000310543.2

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26728 AN: 152096 Hom.: 2759 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.195

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.176 AC: 26729 AN: 152214 Hom.: 2760 Cov.: 33 AF XY: 0.172 AC XY: 12832 AN XY: 74424

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.193

Alfa AF: 0.222 Hom.: 5421

Bravo AF: 0.168

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs861528; hg19: chr14-104182998;