3-45918507-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_024513.4(FYCO1):c.*3257del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.38 (13874 hom., cov: 0)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: FYCO1 NM_024513.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.06

Genes affected

FYCO1 (HGNC:14673): (FYVE and coiled-coil domain autophagy adaptor 1) The gene encodes a Rab7 adapter protein that is implicated in the microtubule transport of autophagosomes. The encoded protein contains a RUN domain, a FYVE-type zinc finger domain, and Golgi dynamics (GOLD) domain. The encoded protein plays a role in microtubule plus end-directed transport of autophagic vesicles through interactions with the small GTPase Rab7, phosphatidylinositol-3-phosphate (PI3P), the autophagosome marker LC3, and the kinesin KIF5. Mutations in this gene are associated with inclusion body myositis (IBM) and autosomal recessive congenital cataracts (CATC2). [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-45918507-TA-T is Benign according to our data. Variant chr3-45918507-TA-T is described in ClinVar as [Benign]. Clinvar id is 345443.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYCO1	NM_024513.4	c.*3257del		3_prime_UTR_variant	18/18	ENST00000296137.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYCO1	ENST00000296137.7	c.*3257del		3_prime_UTR_variant	18/18	1	NM_024513.4	P1
FYCO1	ENST00000433878.5	c.*2910del		3_prime_UTR_variant	7/7	2

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57206 AN: 151776 Hom.: 13838 Cov.: 0

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.375

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.377 AC: 57285 AN: 151894 Hom.: 13874 Cov.: 0 AF XY: 0.369 AC XY: 27437 AN XY: 74256

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.371

Alfa AF: 0.323 Hom.: 1230

Bravo AF: 0.407

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Developmental cataract Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs11349487; hg19: chr3-45959999;