rs10143623

Variant names:

• chr14-103720539-G-A
• rs10143623
• NM_024071.4:c.138+4560G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-103720539-G-A
• chr14-103720539-G-T

Variant summary

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

The NM_024071.4(ZFYVE21):​c.138+4560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,014 control chromosomes in the GnomAD database, including 7,248 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 0.30 (7248 hom., cov: 31)
• Consequence: ZFYVE21 NM_024071.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024071.4. 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
	ZFYVE21	NM_024071.4	MANE Select	c.138+4560G>A		intron	N/A	NP_076976.1	Q9BQ24-1
	ZFYVE21	NM_001198953.2		c.138+4560G>A		intron	N/A	NP_001185882.1	Q9BQ24-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFYVE21	ENST00000311141.7	TSL:1 MANE Select	c.138+4560G>A		intron	N/A	ENSP00000310543.2	Q9BQ24-1
	ZFYVE21	ENST00000944811.1		c.138+4560G>A		intron	N/A	ENSP00000614870.1
	ZFYVE21	ENST00000892139.1		c.138+4560G>A		intron	N/A	ENSP00000562198.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45211 AN: 151898 Hom.: 7246 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.297 AC: 45214 AN: 152014 Hom.: 7248 Cov.: 31 AF XY: 0.291 AC XY: 21608 AN XY: 74304

African (AFR) AF: 0.223 AC: 9261 AN: 41444

American (AMR) AF: 0.255 AC: 3896 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1320 AN: 3470

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4820

European-Finnish (FIN) AF: 0.287 AC: 3033 AN: 10556

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25113 AN: 67966

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.344 Hom.: 1886

Bravo AF: 0.292

Asia WGS AF: 0.123 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10143623; hg19: chr14-104186876;