rs523340

Variant names:

• chr9-109091966-G-A
• rs523340
• NM_032012.4:c.917-811C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-109091966-G-A
• chr9-109091966-G-C
• chr9-109091966-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.917-811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,104 control chromosomes in the GnomAD database, including 921 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 0.10 (921 hom., cov: 33)
• Consequence: TMEM245 NM_032012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 12 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 (SAS) allele frequency at 95% confidence interval = 0.227 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.917-811C>T		intron	N/A	NP_114401.2	Q9H330-2
	TMEM245	NM_001438164.1		c.917-814C>T		intron	N/A	NP_001425093.1
	TMEM245	NM_001438005.1		c.917-811C>T		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.917-811C>T		intron	N/A	ENSP00000363714.3	Q9H330-2
	TMEM245	ENST00000894214.1		c.917-814C>T		intron	N/A	ENSP00000564273.1
	TMEM245	ENST00000952009.1		c.917-817C>T		intron	N/A	ENSP00000622068.1

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15163 AN: 151986 Hom.: 919 Cov.: 33

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0998 AC: 15178 AN: 152104 Hom.: 921 Cov.: 33 AF XY: 0.101 AC XY: 7542 AN XY: 74336

African (AFR) AF: 0.0417 AC: 1732 AN: 41510

American (AMR) AF: 0.0954 AC: 1458 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 338 AN: 3464

East Asian (EAS) AF: 0.129 AC: 669 AN: 5176

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4806

European-Finnish (FIN) AF: 0.0949 AC: 1002 AN: 10554

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8440 AN: 67996

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.116 Hom.: 2537

Bravo AF: 0.0941

Asia WGS AF: 0.168 AC: 584 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.31
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: rs523340; hg19: chr9-111854246;