2-102772135-C-T

Variant names:

• chr2-102772135-C-T
• rs12465996
• NM_144632.5:c.331+7708C>T

Variant summary

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

The NM_144632.5(TMEM182):​c.331+7708C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,174 control chromosomes in the GnomAD database, including 645 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 0.074 (645 hom., cov: 32)
• Consequence: TMEM182 NM_144632.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 3 publications found

Genes affected

TMEM182 (HGNC:26391): (transmembrane protein 182) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144632.5. 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
	TMEM182	NM_144632.5	MANE Select	c.331+7708C>T		intron	N/A	NP_653233.5
	TMEM182	NM_001321343.2		c.202+7708C>T		intron	N/A	NP_001308272.2	B8ZZ71
	TMEM182	NM_001321344.2		c.202+7708C>T		intron	N/A	NP_001308273.2	B8ZZ71

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM182	ENST00000412401.3	TSL:1 MANE Select	c.331+7708C>T		intron	N/A	ENSP00000394178.2	Q6ZP80-1
	TMEM182	ENST00000409173.5	TSL:1	c.202+7708C>T		intron	N/A	ENSP00000387184.1	B8ZZ71
	TMEM182	ENST00000409528.5	TSL:1	c.43+7708C>T		intron	N/A	ENSP00000387258.1	Q6ZP80-2

Frequencies

GnomAD3 genomes AF: 0.0735 AC: 11182 AN: 152056 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.0165

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0735 AC: 11187 AN: 152174 Hom.: 645 Cov.: 32 AF XY: 0.0774 AC XY: 5756 AN XY: 74388

African (AFR) AF: 0.0172 AC: 714 AN: 41532

American (AMR) AF: 0.0912 AC: 1395 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 309 AN: 3468

East Asian (EAS) AF: 0.0242 AC: 125 AN: 5166

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4830

European-Finnish (FIN) AF: 0.210 AC: 2216 AN: 10570

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6039 AN: 68002

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0791 Hom.: 786

Bravo AF: 0.0646

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.37
PhyloP100		-0.86
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: rs12465996; hg19: chr2-103388594;