rs7289126

Variant names:

• chr22-38232300-C-A
• rs7289126
• NM_012264.5:c.359-966G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-38232300-C-A
• chr22-38232300-C-T

Variant summary

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

The NM_012264.5(TMEM184B):​c.359-966G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,074 control chromosomes in the GnomAD database, including 27,381 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 0.58 (27377 hom., cov: 31)
  • Exomes 𝑓: 0.59 (4 hom.)
• Consequence: TMEM184B NM_012264.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 24 publications found

Genes affected

TMEM184B (HGNC:1310): (transmembrane protein 184B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM184B-AS1 (HGNC:56716): (TMEM184B antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012264.5. 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
	TMEM184B	NM_012264.5	MANE Select	c.359-966G>T		intron	N/A	NP_036396.2	Q9Y519
	TMEM184B	NM_001195071.1		c.359-966G>T		intron	N/A	NP_001182000.1	Q9Y519
	TMEM184B	NM_001195072.2		c.161-966G>T		intron	N/A	NP_001182001.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM184B	ENST00000361906.8	TSL:1 MANE Select	c.359-966G>T		intron	N/A	ENSP00000355210.3	Q9Y519
	TMEM184B	ENST00000361684.8	TSL:1	c.359-966G>T		intron	N/A	ENSP00000354441.4	Q9Y519
	TMEM184B	ENST00000436674.5	TSL:1	n.*241-966G>T		intron	N/A	ENSP00000413085.1	F2Z397

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87881 AN: 151934 Hom.: 27310 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.546

GnomAD4 exome AF: 0.591 AC: 13 AN: 22 Hom.: 4 AF XY: 0.500 AC XY: 6 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

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: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.583 AC: 7 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.579 AC: 88015 AN: 152052 Hom.: 27377 Cov.: 31 AF XY: 0.580 AC XY: 43069 AN XY: 74304

African (AFR) AF: 0.821 AC: 34058 AN: 41492

American (AMR) AF: 0.532 AC: 8126 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2349 AN: 5150

South Asian (SAS) AF: 0.629 AC: 3033 AN: 4822

European-Finnish (FIN) AF: 0.470 AC: 4964 AN: 10552

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31983 AN: 67980

Other (OTH) AF: 0.549 AC: 1158 AN: 2108

Alfa AF: 0.502 Hom.: 86376

Bravo AF: 0.589

Asia WGS AF: 0.607 AC: 2116 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	3.1
DANN	Benign	0.86
PhyloP100		0.15
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: rs7289126; hg19: chr22-38628306;