Variant chr2-47024371-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020458.4(TTC7A):c.1641+12G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,600,728 control chromosomes in the GnomAD database, including 18,813 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 1996 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16817 hom. )

Consequence

TTC7A
NM_020458.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.497

Variant links:

Genes affected

TTC7A (HGNC:19750): (tetratricopeptide repeat domain 7A) This gene encodes a protein containing tetratricopeptide repeats. Mutations in this gene disrupt intestinal development and can cause early onset inflammatory bowel disease and intestinal atresia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

TTC7A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 2-47024371-G-C is Benign according to our data. Variant chr2-47024371-G-C is described in ClinVar as [Benign]. Clinvar id is 403574.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC7A	NM_020458.4 linkuse as main transcript	c.1641+12G>C		intron_variant		ENST00000319190.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC7A	ENST00000319190.11 linkuse as main transcript	c.1641+12G>C		intron_variant		2	NM_020458.4	P1	Q9ULT0-1

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24234

AN:

151906

Hom.:

1985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.0811

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.139

AC:

32662

AN:

235468

Hom.:

2355

AF XY:

0.143

AC XY:

18302

AN XY:

127744

show subpopulations

Gnomad AFR exome

AF:

0.200

Gnomad AMR exome

AF:

0.0733

Gnomad ASJ exome

AF:

0.170

Gnomad EAS exome

AF:

0.0773

Gnomad SAS exome

AF:

0.168

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.139

GnomAD4 exome

AF:

0.150

AC:

217189

AN:

1448706

Hom.:

16817

Cov.:

AF XY:

0.151

AC XY:

108961

AN XY:

720240

show subpopulations

Gnomad4 AFR exome

AF:

0.200

Gnomad4 AMR exome

AF:

0.0797

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.0754

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.133

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.153

GnomAD4 genome

AF:

0.160

AC:

24274

AN:

152022

Hom.:

1996

Cov.:

AF XY:

0.157

AC XY:

11673

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.131

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.0805

Gnomad4 SAS

AF:

0.166

Gnomad4 FIN

AF:

0.124

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.109

Hom.:

210

Bravo

AF:

0.158

Asia WGS

AF:

0.133

AC:

463

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Multiple gastrointestinal atresias

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.33

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