Variant 6-43515980-GCAT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2

The NM_015388.4(YIPF3):c.194_196delATG(p.Asp65del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00533 in 1,614,146 control chromosomes in the GnomAD database, including 35 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0055 ( 35 hom. )

Consequence

YIPF3
NM_015388.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.45

Variant links:

Genes affected

YIPF3 (HGNC:21023): (Yip1 domain family member 3) Predicted to be involved in cell differentiation. Located in Golgi apparatus and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

YIPF3 links:

POLR1C (HGNC:20194): (RNA polymerase I and III subunit C) The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

POLR1C links:

YIPF3 (HGNC:):

YIPF3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_015388.4

BP6

Variant 6-43515980-GCAT-G is Benign according to our data. Variant chr6-43515980-GCAT-G is described in ClinVar as [Likely_benign]. Clinvar id is 3388171.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 35 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YIPF3	NM_015388.4 linkuse as main transcript	c.194_196delATG	p.Asp65del	disruptive_inframe_deletion	2/9	ENST00000372422.7	NP_056203.2	Q9GZM5
YIPF3	XM_047418608.1 linkuse as main transcript	c.89_91delATG	p.Asp30del	disruptive_inframe_deletion	2/9		XP_047274564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YIPF3	ENST00000372422.7 linkuse as main transcript	c.194_196delATG	p.Asp65del	disruptive_inframe_deletion	2/9	1	NM_015388.4	ENSP00000361499.2		Q9GZM5

Frequencies

GnomAD3 genomes

AF:

0.00370

AC:

563

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00503

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00430

AC:

1080

AN:

251308

Hom.:

AF XY:

0.00440

AC XY:

598

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000925

Gnomad ASJ exome

AF:

0.0119

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00323

Gnomad FIN exome

AF:

0.0133

Gnomad NFE exome

AF:

0.00447

Gnomad OTH exome

AF:

0.00489

GnomAD4 exome

AF:

0.00550

AC:

8044

AN:

1461816

Hom.:

AF XY:

0.00547

AC XY:

3979

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.000961

Gnomad4 ASJ exome

AF:

0.0118

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00300

Gnomad4 FIN exome

AF:

0.0123

Gnomad4 NFE exome

AF:

0.00582

Gnomad4 OTH exome

AF:

0.00455

GnomAD4 genome

AF:

0.00370

AC:

563

AN:

152330

Hom.:

Cov.:

AF XY:

0.00407

AC XY:

303

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000722

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.0122

Gnomad4 NFE

AF:

0.00503

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00393

Hom.:

Bravo

AF:

0.00265

EpiCase

AF:

0.00420

EpiControl

AF:

0.00421

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

YIPF3: PM4:Supporting, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over