rs789852

Variant names:

• chr3-194606369-T-C
• rs789852
• NM_001011655.3:c.1018-1924A>G

Variant summary

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

The NM_001166305.2(TMEM44):​c.1159-1924A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,252 control chromosomes in the GnomAD database, including 66,173 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 0.93 (66173 hom., cov: 31)
• Consequence: TMEM44 NM_001166305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 16 publications found

Genes affected

TMEM44 (HGNC:25120): (transmembrane protein 44) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105374291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166305.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM44	NM_001011655.3	MANE Select	c.1018-1924A>G		intron	N/A	NP_001011655.1
	TMEM44	NM_001166305.2		c.1159-1924A>G		intron	N/A	NP_001159777.1
	TMEM44	NM_138399.5		c.1018-1924A>G		intron	N/A	NP_612408.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM44	ENST00000347147.9	TSL:1 MANE Select	c.1018-1924A>G		intron	N/A	ENSP00000333355.6
	TMEM44	ENST00000392432.6	TSL:1	c.1159-1924A>G		intron	N/A	ENSP00000376227.2
	TMEM44	ENST00000473092.5	TSL:1	c.1018-1924A>G		intron	N/A	ENSP00000418674.1

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141752 AN: 152134 Hom.: 66105 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.932 AC: 141880 AN: 152252 Hom.: 66173 Cov.: 31 AF XY: 0.934 AC XY: 69509 AN XY: 74432

African (AFR) AF: 0.960 AC: 39877 AN: 41550

American (AMR) AF: 0.929 AC: 14181 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5110 AN: 5170

South Asian (SAS) AF: 0.930 AC: 4496 AN: 4832

European-Finnish (FIN) AF: 0.952 AC: 10101 AN: 10608

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61852 AN: 68032

Other (OTH) AF: 0.925 AC: 1956 AN: 2114

Alfa AF: 0.913 Hom.: 260246

Bravo AF: 0.932

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.072
DANN	Benign	0.47
PhyloP100		-1.3
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: rs789852; hg19: chr3-194327098;