Variant 10-17771268-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001098844.3(TMEM236):c.258-41T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 1,579,420 control chromosomes in the GnomAD database, including 2,167 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 0.042 ( 262 hom., cov: 33)

Exomes 𝑓: 0.031 ( 1905 hom. )

Consequence

TMEM236
NM_001098844.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.175

Variant links:

Genes affected

TMEM236 (HGNC:23473): (transmembrane protein 236) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM236 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM236	NM_001098844.3 linkuse as main transcript	c.258-41T>G		intron_variant		ENST00000377495.2
TMEM236	XM_017016574.2 linkuse as main transcript	c.72-41T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM236	ENST00000377495.2 linkuse as main transcript	c.258-41T>G		intron_variant		2	NM_001098844.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0417

AC:

6347

AN:

152202

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0493

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.0522

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0125

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0187

Gnomad OTH

AF:

0.0401

GnomAD3 exomes

AF:

0.0619

AC:

9806

AN:

158416

Hom.:

825

AF XY:

0.0622

AC XY:

5342

AN XY:

85858

show subpopulations

Gnomad AFR exome

AF:

0.0525

Gnomad AMR exome

AF:

0.0620

Gnomad ASJ exome

AF:

0.0876

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.0175

Gnomad NFE exome

AF:

0.0236

Gnomad OTH exome

AF:

0.0484

GnomAD4 exome

AF:

0.0311

AC:

44336

AN:

1427100

Hom.:

1905

Cov.:

AF XY:

0.0331

AC XY:

23575

AN XY:

712580

show subpopulations

Gnomad4 AFR exome

AF:

0.0506

Gnomad4 AMR exome

AF:

0.0551

Gnomad4 ASJ exome

AF:

0.0805

Gnomad4 EAS exome

AF:

0.209

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.0152

Gnomad4 NFE exome

AF:

0.0161

Gnomad4 OTH exome

AF:

0.0422

GnomAD4 genome

AF:

0.0417

AC:

6349

AN:

152320

Hom.:

262

Cov.:

AF XY:

0.0444

AC XY:

3311

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0494

Gnomad4 AMR

AF:

0.0523

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.209

Gnomad4 SAS

AF:

0.119

Gnomad4 FIN

AF:

0.0125

Gnomad4 NFE

AF:

0.0187

Gnomad4 OTH

AF:

0.0392

Alfa

AF:

0.0387

Hom.:

102

Bravo

AF:

0.0434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.78

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over