6-130418356-A-C

Position:

• chr6-130418356-A-C

Variant summary

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

The NM_001258277.2(TMEM200A):​c.-16-22051A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,152 control chromosomes in the GnomAD database, including 2,199 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 0.16 (2199 hom., cov: 32)
• Consequence: TMEM200A NM_001258277.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

TMEM200A (HGNC:21075): (transmembrane protein 200A) 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM200A	NM_001258277.2	c.-16-22051A>C		intron_variant		ENST00000296978.4	NP_001245206.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM200A	ENST00000296978.4	c.-16-22051A>C		intron_variant		1	NM_001258277.2	ENSP00000296978.3
TMEM200A	ENST00000617887.4	c.-16-22051A>C		intron_variant		2		ENSP00000480294.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24985 AN: 152034 Hom.: 2194 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.168

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.164 AC: 25004 AN: 152152 Hom.: 2199 Cov.: 32 AF XY: 0.169 AC XY: 12553 AN XY: 74392

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.172

Alfa AF: 0.146 Hom.: 3329

Bravo AF: 0.169

Asia WGS AF: 0.302 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.85

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: rs12190331; hg19: chr6-130739501;