3-45934491-A-G

Variant names:

• chr3-45934491-A-G
• rs1072755
• NM_024513.4:c.4040+1957T>C

Variant summary

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

The NM_024513.4(FYCO1):​c.4040+1957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,138 control chromosomes in the GnomAD database, including 11,797 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 0.38 (11797 hom., cov: 33)
• Consequence: FYCO1 NM_024513.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 9 publications found

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]

FYCO1 Gene-Disease associations (from GenCC):

• cataract 18

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• early-onset nuclear cataract

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• total early-onset cataract

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024513.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYCO1	NM_024513.4	MANE Select	c.4040+1957T>C		intron	N/A	NP_078789.2
	FYCO1	NM_001386421.1		c.4040+1957T>C		intron	N/A	NP_001373350.1
	FYCO1	NM_001386422.1		c.4040+1957T>C		intron	N/A	NP_001373351.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYCO1	ENST00000296137.7	TSL:1 MANE Select	c.4040+1957T>C		intron	N/A	ENSP00000296137.2
	FYCO1	ENST00000433878.5	TSL:2	c.404+1957T>C		intron	N/A	ENSP00000388136.1
	FYCO1	ENST00000438446.1	TSL:5	c.53+1957T>C		intron	N/A	ENSP00000398517.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57429 AN: 152020 Hom.: 11780 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.378 AC: 57479 AN: 152138 Hom.: 11797 Cov.: 33 AF XY: 0.384 AC XY: 28543 AN XY: 74356

African (AFR) AF: 0.254 AC: 10539 AN: 41510

American (AMR) AF: 0.519 AC: 7933 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1344 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3410 AN: 5178

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4828

European-Finnish (FIN) AF: 0.438 AC: 4631 AN: 10568

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26637 AN: 67978

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.391 Hom.: 37905

Bravo AF: 0.378

Asia WGS AF: 0.519 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-3.0
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: rs1072755; hg19: chr3-45975983;