3-100536438-A-G

Position:

• chr3-100536438-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

TMEM45A (HGNC:25480): (transmembrane protein 45A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM45A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TMEM45A	NM_018004.3	c.-3-18771A>G		intron_variant		ENST00000323523.8	NP_060474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM45A	ENST00000323523.8	c.-3-18771A>G		intron_variant		1	NM_018004.3	ENSP00000319009.4
TMEM45A	ENST00000403410.5	c.45+16830A>G		intron_variant		5		ENSP00000385089.1
TMEM45A	ENST00000449609.1	c.45+16830A>G		intron_variant		3		ENSP00000405597.1
TMEM45A	ENST00000462884.1	n.154+16830A>G		intron_variant		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

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.404

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

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: rs6799992; hg19: chr3-100255282;