rs789852

chr3-194606369-T-C

Variant summary

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

The NM_001011655.3(TMEM44):c.1018-1924A>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_001011655.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM44	NM_001011655.3	c.1018-1924A>G		intron_variant		ENST00000347147.9
LOC105374291	XR_007096222.1	n.2822T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM44	ENST00000347147.9	c.1018-1924A>G		intron_variant		1	NM_001011655.3	P2

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

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.925

Alfa AF: 0.909 Hom.: 132694

Bravo AF: 0.932

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.072
Dann	Benign	0.47

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: rs789852; hg19: chr3-194327098;