rs10484278

Variant names:

• chr6-129856681-A-G
• rs10484278
• NM_001010876.2:c.33+4475T>C

Variant summary

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

The NM_001010876.2(TMEM244):​c.33+4475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,162 control chromosomes in the GnomAD database, including 428 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 0.062 (428 hom., cov: 32)
• Consequence: TMEM244 NM_001010876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 3 publications found

Genes affected

TMEM244 (HGNC:21571): (transmembrane protein 244) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105377999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM244	NM_001010876.2	c.33+4475T>C		intron_variant	Intron 1 of 4	ENST00000368143.6	NP_001010876.1
LOC105377999	XR_942986.3	n.85+969A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM244	ENST00000368143.6	c.33+4475T>C		intron_variant	Intron 1 of 4	2	NM_001010876.2	ENSP00000357125.1
TMEM244	ENST00000438392.3	c.33+4475T>C		intron_variant	Intron 2 of 5	5		ENSP00000403755.1

Frequencies

GnomAD3 genomes AF: 0.0619 AC: 9419 AN: 152044 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0471

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0619 AC: 9426 AN: 152162 Hom.: 428 Cov.: 32 AF XY: 0.0630 AC XY: 4682 AN XY: 74372

African (AFR) AF: 0.0945 AC: 3926 AN: 41536

American (AMR) AF: 0.0312 AC: 476 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4824

European-Finnish (FIN) AF: 0.0323 AC: 342 AN: 10590

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0471 AC: 3198 AN: 67954

Other (OTH) AF: 0.0567 AC: 120 AN: 2116

Alfa AF: 0.0657 Hom.: 54

Bravo AF: 0.0595

Asia WGS AF: 0.0920 AC: 319 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.77
PhyloP100		0.35
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: rs10484278; hg19: chr6-130177826;