rs1044905

chr9-109019215-G-Achr9-109019215-G-Cchr9-109019215-G-T

Variant summary

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

The NM_032012.4(TMEM245):c.*1245C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,078 control chromosomes in the GnomAD database, including 4,497 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 0.22 (4495 hom., cov: 31)
  • Exomes 𝑓: 0.25 (2 hom.)
• Consequence: TMEM245 NM_032012.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

TMEM245 (HGNC:1363): (transmembrane protein 245) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM245	NM_032012.4	c.*1245C>T		3_prime_UTR_variant	18/18	ENST00000374586.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM245	ENST00000374586.8	c.*1245C>T		3_prime_UTR_variant	18/18	1	NM_032012.4	P3
TMEM245	ENST00000472207.5	n.2972C>T		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33441 AN: 151918 Hom.: 4492 Cov.: 31

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.250 AC: 10 AN: 40 Hom.: 2 Cov.: 0 AF XY: 0.219 AC XY: 7 AN XY: 32

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.220 AC: 33452 AN: 152038 Hom.: 4495 Cov.: 31 AF XY: 0.222 AC XY: 16462 AN XY: 74318

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.242

Alfa AF: 0.225 Hom.: 1838

Bravo AF: 0.213

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1044905; hg19: chr9-111781495;