chr22-38219529-A-T

Position:

• chr22-38219529-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012264.5(TMEM184B):​c.*1940T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 874,882 control chromosomes in the GnomAD database, including 194,548 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 0.75 (41825 hom., cov: 29)
  • Exomes 𝑓: 0.70 (152723 hom.)
• Consequence: TMEM184B NM_012264.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM184B	NM_012264.5	c.*1940T>A		3_prime_UTR_variant	9/9	ENST00000361906.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM184B	ENST00000361906.8	c.*1940T>A		3_prime_UTR_variant	9/9	1	NM_012264.5	P1
TMEM184B	ENST00000361684.8	c.*1940T>A		3_prime_UTR_variant	9/9	1		P1
TMEM184B	ENST00000436674.5	c.*3046T>A		3_prime_UTR_variant, NMD_transcript_variant	10/10	1
TMEM184B	ENST00000633056.1	n.4575T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 111874 AN: 149826 Hom.: 41795 Cov.: 29

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.696 AC: 504785 AN: 724966 Hom.: 152723 Cov.: 48 AF XY: 0.697 AC XY: 233228 AN XY: 334716

Gnomad4 AFR exome AF: 0.747

Gnomad4 AMR exome AF: 0.715

Gnomad4 ASJ exome AF: 0.693

Gnomad4 EAS exome AF: 0.709

Gnomad4 SAS exome AF: 0.661

Gnomad4 FIN exome AF: 0.733

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 0.695

GnomAD4 genome AF: 0.747 AC: 111950 AN: 149916 Hom.: 41825 Cov.: 29 AF XY: 0.746 AC XY: 54539 AN XY: 73152

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.727

Alfa AF: 0.718 Hom.: 4049

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.13
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs1059804; hg19: chr22-38615536;