Variant 1-16059513-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_182623.3(FAM131C):c.543A>G(p.Gln181Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 1,590,146 control chromosomes in the GnomAD database, including 446,535 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37338 hom., cov: 29)

Exomes 𝑓: 0.75 ( 409197 hom. )

Consequence

FAM131C
NM_182623.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.530

Variant links:

Genes affected

FAM131C (HGNC:26717): (family with sequence similarity 131 member C)

FAM131C links:

FAM131C (HGNC:):

FAM131C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 1-16059513-T-C is Benign according to our data. Variant chr1-16059513-T-C is described in ClinVar as [Benign]. Clinvar id is 1240760.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM131C	NM_182623.3 linkuse as main transcript	c.543A>G	p.Gln181Gln	synonymous_variant	6/7	ENST00000375662.5	NP_872429.2	Q96AQ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM131C	ENST00000375662.5 linkuse as main transcript	c.543A>G	p.Gln181Gln	synonymous_variant	6/7	1	NM_182623.3	ENSP00000364814.4		Q96AQ9
FAM131C	ENST00000494078.1 linkuse as main transcript	n.617A>G		non_coding_transcript_exon_variant	5/6	3

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

105879

AN:

150510

Hom.:

37327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.544

Gnomad AMI

AF:

0.761

Gnomad AMR

AF:

0.810

Gnomad ASJ

AF:

0.753

Gnomad EAS

AF:

0.826

Gnomad SAS

AF:

0.816

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.799

Gnomad NFE

AF:

0.756

Gnomad OTH

AF:

0.757

GnomAD3 exomes

AF:

0.765

AC:

180757

AN:

236330

Hom.:

69614

AF XY:

0.768

AC XY:

98863

AN XY:

128712

show subpopulations

Gnomad AFR exome

AF:

0.524

Gnomad AMR exome

AF:

0.869

Gnomad ASJ exome

AF:

0.770

Gnomad EAS exome

AF:

0.825

Gnomad SAS exome

AF:

0.814

Gnomad FIN exome

AF:

0.671

Gnomad NFE exome

AF:

0.758

Gnomad OTH exome

AF:

0.774

GnomAD4 exome

AF:

0.753

AC:

1084590

AN:

1439518

Hom.:

409197

Cov.:

AF XY:

0.756

AC XY:

540372

AN XY:

714428

show subpopulations

Gnomad4 AFR exome

AF:

0.521

Gnomad4 AMR exome

AF:

0.856

Gnomad4 ASJ exome

AF:

0.763

Gnomad4 EAS exome

AF:

0.840

Gnomad4 SAS exome

AF:

0.812

Gnomad4 FIN exome

AF:

0.678

Gnomad4 NFE exome

AF:

0.752

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.703

AC:

105933

AN:

150628

Hom.:

37338

Cov.:

AF XY:

0.705

AC XY:

51836

AN XY:

73526

show subpopulations

Gnomad4 AFR

AF:

0.544

Gnomad4 AMR

AF:

0.811

Gnomad4 ASJ

AF:

0.753

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.817

Gnomad4 FIN

AF:

0.683

Gnomad4 NFE

AF:

0.756

Gnomad4 OTH

AF:

0.756

Alfa

AF:

0.739

Hom.:

14545

Asia WGS

AF:

0.767

AC:

2664

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.1

DANN

Benign

0.64

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