rs643410

Variant names:

• chr9-109037283-A-C
• rs643410
• NM_032012.4:c.2224+734T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-109037283-A-C
• chr9-109037283-A-G
• chr9-109037283-A-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.2224+734T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,236 control chromosomes in the GnomAD database, including 66,235 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 0.93 (66235 hom., cov: 32)
• Consequence: TMEM245 NM_032012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.2224+734T>G		intron	N/A	NP_114401.2	Q9H330-2
	TMEM245	NM_001438164.1		c.2221+734T>G		intron	N/A	NP_001425093.1
	TMEM245	NM_001438005.1		c.2200+734T>G		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.2224+734T>G		intron	N/A	ENSP00000363714.3	Q9H330-2
	TMEM245	ENST00000894214.1		c.2221+734T>G		intron	N/A	ENSP00000564273.1
	TMEM245	ENST00000952009.1		c.2218+734T>G		intron	N/A	ENSP00000622068.1

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141791 AN: 152118 Hom.: 66175 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.932 AC: 141912 AN: 152236 Hom.: 66235 Cov.: 32 AF XY: 0.933 AC XY: 69437 AN XY: 74422

African (AFR) AF: 0.897 AC: 37265 AN: 41530

American (AMR) AF: 0.951 AC: 14553 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5184 AN: 5188

South Asian (SAS) AF: 0.971 AC: 4686 AN: 4824

European-Finnish (FIN) AF: 0.924 AC: 9786 AN: 10592

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63857 AN: 68016

Other (OTH) AF: 0.939 AC: 1982 AN: 2110

Alfa AF: 0.940 Hom.: 7034

Bravo AF: 0.930

Asia WGS AF: 0.978 AC: 3401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.80
PhyloP100		-0.27
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs643410;

hg19: chr9-111799563;