Variant chr6-43516856-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_015388.4(YIPF3):c.-49C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,548,304 control chromosomes in the GnomAD database, including 392 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.016 ( 33 hom., cov: 33)

Exomes 𝑓: 0.021 ( 359 hom. )

Consequence

YIPF3
NM_015388.4 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0290

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-43516856-G-A is Benign according to our data. Variant chr6-43516856-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1201016.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0163 (2488/152394) while in subpopulation NFE AF= 0.0262 (1786/68040). AF 95% confidence interval is 0.0252. There are 33 homozygotes in gnomad4. There are 1178 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YIPF3	NM_015388.4 linkuse as main transcript	c.-49C>T		5_prime_UTR_variant	1/9	ENST00000372422.7
YIPF3	XM_047418608.1 linkuse as main transcript	c.-480C>T		5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YIPF3	ENST00000372422.7 linkuse as main transcript	c.-49C>T		5_prime_UTR_variant	1/9	1	NM_015388.4	P2

Frequencies

GnomAD3 genomes

AF:

0.0163

AC:

2489

AN:

152276

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00357

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0132

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.0248

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0263

Gnomad OTH

AF:

0.0148

GnomAD3 exomes

AF:

0.0149

AC:

2380

AN:

159786

Hom.:

AF XY:

0.0142

AC XY:

1210

AN XY:

85000

show subpopulations

Gnomad AFR exome

AF:

0.00284

Gnomad AMR exome

AF:

0.00847

Gnomad ASJ exome

AF:

0.00365

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00222

Gnomad FIN exome

AF:

0.0262

Gnomad NFE exome

AF:

0.0245

Gnomad OTH exome

AF:

0.0195

GnomAD4 exome

AF:

0.0214

AC:

29808

AN:

1395910

Hom.:

359

Cov.:

AF XY:

0.0207

AC XY:

14302

AN XY:

689360

show subpopulations

Gnomad4 AFR exome

AF:

0.00325

Gnomad4 AMR exome

AF:

0.00881

Gnomad4 ASJ exome

AF:

0.00410

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00232

Gnomad4 FIN exome

AF:

0.0273

Gnomad4 NFE exome

AF:

0.0248

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0163

AC:

2488

AN:

152394

Hom.:

Cov.:

AF XY:

0.0158

AC XY:

1178

AN XY:

74530

show subpopulations

Gnomad4 AFR

AF:

0.00356

Gnomad4 AMR

AF:

0.0132

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00310

Gnomad4 FIN

AF:

0.0248

Gnomad4 NFE

AF:

0.0262

Gnomad4 OTH

AF:

0.0147

Alfa

AF:

0.00689

Hom.:

Bravo

AF:

0.0143

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

GeneDx

Jul 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.2

DANN

Benign

0.87

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