chr11-120328019-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001198671.2(TLCD5):​c.199+379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,032 control chromosomes in the GnomAD database, including 2,938 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 2938 hom., cov: 32)

Consequence

TLCD5
NM_001198671.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950
Variant links:
Genes affected
TLCD5 (HGNC:28280): (TLC domain containing 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TLCD5NM_001198671.2 linkuse as main transcriptc.199+379A>G intron_variant ENST00000375095.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TLCD5ENST00000375095.3 linkuse as main transcriptc.199+379A>G intron_variant 2 NM_001198671.2 P1Q6ZRR5-1
TLCD5ENST00000529187.1 linkuse as main transcriptc.265+379A>G intron_variant 1 Q6ZRR5-4
TLCD5ENST00000314475.6 linkuse as main transcriptc.265+379A>G intron_variant 2 Q6ZRR5-3
TLCD5ENST00000531346.1 linkuse as main transcriptn.74-1958A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.192
AC:
29099
AN:
151914
Hom.:
2932
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.0482
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.172
Gnomad EAS
AF:
0.200
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.244
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.162
Gnomad OTH
AF:
0.166
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.192
AC:
29134
AN:
152032
Hom.:
2938
Cov.:
32
AF XY:
0.195
AC XY:
14526
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.234
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.172
Gnomad4 EAS
AF:
0.200
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.244
Gnomad4 NFE
AF:
0.162
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.164
Hom.:
2022
Bravo
AF:
0.186
Asia WGS
AF:
0.251
AC:
874
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.29
DANN
Benign
0.67

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: rs11827818; hg19: chr11-120198728; API