chr9-109098517-C-T

Variant names:

• chr9-109098517-C-T
• rs1519466
• NM_032012.4:c.800-4926G>A

Variant summary

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

The NM_032012.4(TMEM245):​c.800-4926G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 151,796 control chromosomes in the GnomAD database, including 61,750 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 0.90 (61750 hom., cov: 28)
• Consequence: TMEM245 NM_032012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM245	NM_032012.4	MANE Select	c.800-4926G>A		intron	N/A	NP_114401.2	Q9H330-2
	TMEM245	NM_001438164.1		c.800-4926G>A		intron	N/A	NP_001425093.1
	TMEM245	NM_001438005.1		c.800-4926G>A		intron	N/A	NP_001424934.1	H7C0G1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM245	ENST00000374586.8	TSL:1 MANE Select	c.800-4926G>A		intron	N/A	ENSP00000363714.3	Q9H330-2
	TMEM245	ENST00000894214.1		c.800-4926G>A		intron	N/A	ENSP00000564273.1
	TMEM245	ENST00000952009.1		c.800-4926G>A		intron	N/A	ENSP00000622068.1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136641 AN: 151680 Hom.: 61705 Cov.: 28

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.901 AC: 136742 AN: 151796 Hom.: 61750 Cov.: 28 AF XY: 0.899 AC XY: 66705 AN XY: 74206

African (AFR) AF: 0.958 AC: 39687 AN: 41408

American (AMR) AF: 0.904 AC: 13783 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3132 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4506 AN: 5176

South Asian (SAS) AF: 0.756 AC: 3641 AN: 4814

European-Finnish (FIN) AF: 0.905 AC: 9459 AN: 10454

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59610 AN: 67918

Other (OTH) AF: 0.904 AC: 1905 AN: 2108

Alfa AF: 0.880 Hom.: 33108

Bravo AF: 0.906

Asia WGS AF: 0.828 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.11
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: rs1519466; hg19: chr9-111860797;