20-6075395-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017671.5(FERMT1):​c.*1777_*1778insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 76169 hom., cov: 0)
Exomes 𝑓: 1.0 ( 71 hom. )

Consequence

FERMT1
NM_017671.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.234
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 20-6075395-T-TA is Benign according to our data. Variant chr20-6075395-T-TA is described in ClinVar as [Benign]. Clinvar id is 339178.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FERMT1NM_017671.5 linkuse as main transcriptc.*1777_*1778insT 3_prime_UTR_variant 15/15 ENST00000217289.9 NP_060141.3
FERMT1XM_024451935.2 linkuse as main transcriptc.*1777_*1778insT 3_prime_UTR_variant 15/15 XP_024307703.1
FERMT1XM_047440259.1 linkuse as main transcriptc.*1777_*1778insT 3_prime_UTR_variant 15/15 XP_047296215.1
FERMT1XM_047440260.1 linkuse as main transcriptc.*1777_*1778insT 3_prime_UTR_variant 14/14 XP_047296216.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FERMT1ENST00000217289.9 linkuse as main transcriptc.*1777_*1778insT 3_prime_UTR_variant 15/151 NM_017671.5 ENSP00000217289 P1Q9BQL6-1
FERMT1ENST00000478194.1 linkuse as main transcriptn.2771_2772insT non_coding_transcript_exon_variant 7/71

Frequencies

GnomAD3 genomes
AF:
1.00
AC:
152220
AN:
152220
Hom.:
76110
Cov.:
0
show subpopulations
Gnomad AFR
AF:
1.00
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
1.00
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
1.00
GnomAD4 exome
AF:
1.00
AC:
142
AN:
142
Hom.:
71
Cov.:
0
AF XY:
1.00
AC XY:
80
AN XY:
80
show subpopulations
Gnomad4 EAS exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
GnomAD4 genome
AF:
1.00
AC:
152338
AN:
152338
Hom.:
76169
Cov.:
0
AF XY:
1.00
AC XY:
74496
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
1.00
Gnomad4 AMR
AF:
1.00
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
1.00
Alfa
AF:
1.00
Hom.:
8166
Bravo
AF:
1.00
Asia WGS
AF:
1.00
AC:
3478
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Kindler syndrome Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 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.

Other links and lift over

dbSNP: rs397756084; hg19: chr20-6056042; API