rs1044905

Variant names:

• chr9-109019215-G-A
• rs1044905
• NM_032012.4:c.*1245C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-109019215-G-A
• chr9-109019215-G-C
• chr9-109019215-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032012.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM245	NM_032012.4	MANE Select	c.*1245C>T		3_prime_UTR	Exon 18 of 18	NP_114401.2
	TMEM245	NM_001438164.1		c.*1245C>T		3_prime_UTR	Exon 18 of 18	NP_001425093.1
	TMEM245	NM_001438005.1		c.*1245C>T		3_prime_UTR	Exon 17 of 17	NP_001424934.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM245	ENST00000374586.8	TSL:1 MANE Select	c.*1245C>T		3_prime_UTR	Exon 18 of 18	ENSP00000363714.3
	TMEM245	ENST00000472207.5	TSL:2	n.2972C>T		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.267 AC: 8 AN: 30

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.0527 AC: 2187 AN: 41502

American (AMR) AF: 0.300 AC: 4579 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1469 AN: 5168

South Asian (SAS) AF: 0.191 AC: 921 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3130 AN: 10556

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19340 AN: 67942

Other (OTH) AF: 0.242 AC: 511 AN: 2108

Alfa AF: 0.228 Hom.: 2225

Bravo AF: 0.213

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1044905; hg19: chr9-111781495;