rs6799992

Variant names:

• chr3-100536438-A-G
• rs6799992
• NM_018004.3:c.-3-18771A>G

Variant summary

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

The NM_018004.3(TMEM45A):​c.-3-18771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,110 control chromosomes in the GnomAD database, including 10,689 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 0.36 (10689 hom., cov: 32)
• Consequence: TMEM45A NM_018004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 4 publications found

Genes affected

TMEM45A (HGNC:25480): (transmembrane protein 45A) Predicted to be integral component of membrane. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM45A	NM_018004.3	c.-3-18771A>G		intron_variant	Intron 1 of 5	ENST00000323523.8	NP_060474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM45A	ENST00000323523.8	c.-3-18771A>G		intron_variant	Intron 1 of 5	1	NM_018004.3	ENSP00000319009.4
TMEM45A	ENST00000403410.5	c.45+16830A>G		intron_variant	Intron 3 of 7	5		ENSP00000385089.1
TMEM45A	ENST00000449609.1	c.45+16830A>G		intron_variant	Intron 2 of 4	3		ENSP00000405597.1
TMEM45A	ENST00000462884.1	n.154+16830A>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54862 AN: 151992 Hom.: 10693 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.361 AC: 54886 AN: 152110 Hom.: 10689 Cov.: 32 AF XY: 0.362 AC XY: 26947 AN XY: 74358

African (AFR) AF: 0.214 AC: 8904 AN: 41518

American (AMR) AF: 0.433 AC: 6612 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5172

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4810

European-Finnish (FIN) AF: 0.442 AC: 4676 AN: 10578

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28513 AN: 67970

Other (OTH) AF: 0.404 AC: 854 AN: 2112

Alfa AF: 0.378 Hom.: 1962

Bravo AF: 0.361

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		0.029
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: rs6799992; hg19: chr3-100255282;