Variant 20-6075049-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_017671.5(FERMT1):c.*2123_*2124insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 129,034 control chromosomes in the GnomAD database, including 1,956 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.17 ( 1956 hom., cov: 22)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

FERMT1
NM_017671.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.184

Variant links:

Genes affected

FERMT1 (HGNC:15889): (FERM domain containing kindlin 1) This gene encodes a member of the fermitin family, and contains a FERM domain and a pleckstrin homology domain. The encoded protein is involved in integrin signaling and linkage of the actin cytoskeleton to the extracellular matrix. Mutations in this gene have been linked to Kindler syndrome. [provided by RefSeq, Dec 2009]

FERMT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
FERMT1	NM_017671.5 linkuse as main transcript	c.2123_2124insA	3_prime_UTR_variant	15/15	ENST00000217289.9
FERMT1	XM_024451935.2 linkuse as main transcript	c.2123_2124insA	3_prime_UTR_variant	15/15
FERMT1	XM_047440259.1 linkuse as main transcript	c.2123_2124insA	3_prime_UTR_variant	15/15
FERMT1	XM_047440260.1 linkuse as main transcript	c.2123_2124insA	3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FERMT1	ENST00000217289.9 linkuse as main transcript	c.2123_2124insA		3_prime_UTR_variant	15/15	1	NM_017671.5	P1	Q9BQL6-1
FERMT1	ENST00000478194.1 linkuse as main transcript	n.3117_3118insA		non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

21527

AN:

128952

Hom.:

1954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.00935

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.116

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.138

GnomAD4 exome

AF:

0.136

AC:

AN:

Hom.:

Cov.:

AF XY:

0.194

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.136

GnomAD4 genome

AF:

0.167

AC:

21532

AN:

128968

Hom.:

1956

Cov.:

AF XY:

0.168

AC XY:

10440

AN XY:

62024

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.00938

Gnomad4 SAS

AF:

0.129

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.136

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Kindler syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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