chr11-120328019-A-G

Position:

• chr11-120328019-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

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

ACMG classification

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
TLCD5	NM_001198671.2	c.199+379A>G		intron_variant		ENST00000375095.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLCD5	ENST00000375095.3	c.199+379A>G		intron_variant		2	NM_001198671.2	P1
TLCD5	ENST00000529187.1	c.265+379A>G		intron_variant		1
TLCD5	ENST00000314475.6	c.265+379A>G		intron_variant		2
TLCD5	ENST00000531346.1	n.74-1958A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29099 AN: 151914 Hom.: 2932 Cov.: 32

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

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

Other links and lift over

dbSNP: rs11827818; hg19: chr11-120198728;