rs275838

Variant names:

• chr19-48362957-C-A
• rs275838
• NM_018273.4:c.264+334G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48362957-C-A
• chr19-48362957-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018273.4(TMEM143):​c.264+334G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,052 control chromosomes in the GnomAD database, including 38,017 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 0.70 (38017 hom., cov: 33)
• Consequence: TMEM143 NM_018273.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 10 publications found

Genes affected

TMEM143 (HGNC:25603): (transmembrane protein 143) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM143	NM_018273.4	c.264+334G>T		intron_variant	Intron 2 of 7	ENST00000293261.8	NP_060743.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM143	ENST00000293261.8	c.264+334G>T		intron_variant	Intron 2 of 7	1	NM_018273.4	ENSP00000293261.2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106471 AN: 151932 Hom.: 37990 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.701 AC: 106544 AN: 152052 Hom.: 38017 Cov.: 33 AF XY: 0.702 AC XY: 52158 AN XY: 74318

African (AFR) AF: 0.557 AC: 23089 AN: 41426

American (AMR) AF: 0.808 AC: 12337 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4312 AN: 5192

South Asian (SAS) AF: 0.766 AC: 3696 AN: 4828

European-Finnish (FIN) AF: 0.713 AC: 7537 AN: 10568

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50334 AN: 67990

Other (OTH) AF: 0.738 AC: 1558 AN: 2112

Alfa AF: 0.734 Hom.: 53545

Bravo AF: 0.701

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.58
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs275838; hg19: chr19-48866214;