rs964132

Variant names:

• chr19-19132366-C-T
• rs964132
• NM_017814.3:c.429G>A
• TMEM161A p.Thr143Thr

Your query was ambiguous. Multiple possible variants found:

• chr19-19132366-C-T
• chr19-19132366-C-A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_017814.3(TMEM161A):​c.429G>A​(p.Thr143Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.039 in 1,613,058 control chromosomes in the GnomAD database, including 3,716 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.042 (425 hom., cov: 33)
  • Exomes 𝑓: 0.039 (3291 hom.)
• Consequence: TMEM161A NM_017814.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36
• Publications: 11 publications found

Genes affected

TMEM161A (HGNC:26020): (transmembrane protein 161A) Involved in several processes, including cellular response to UV; regulation of response to DNA damage stimulus; and response to retinoic acid. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP7: Synonymous conserved (PhyloP=-3.36 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017814.3. 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
	TMEM161A	NM_017814.3	MANE Select	c.429G>A	p.Thr143Thr	synonymous	Exon 5 of 12	NP_060284.1	Q9NX61-1
	TMEM161A	NM_001411131.1		c.354G>A	p.Thr118Thr	synonymous	Exon 5 of 12	NP_001398060.1	K7EPA3
	TMEM161A	NM_001256766.3		c.286+291G>A		intron	N/A	NP_001243695.1	Q9NX61-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM161A	ENST00000162044.14	TSL:1 MANE Select	c.429G>A	p.Thr143Thr	synonymous	Exon 5 of 12	ENSP00000162044.7	Q9NX61-1
	TMEM161A	ENST00000913782.1		c.429G>A	p.Thr143Thr	synonymous	Exon 5 of 12	ENSP00000583841.1
	TMEM161A	ENST00000877801.1		c.429G>A	p.Thr143Thr	synonymous	Exon 5 of 12	ENSP00000547860.1

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6383 AN: 152122 Hom.: 425 Cov.: 33

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0339

GnomAD2 exomes AF: 0.0679 AC: 16970 AN: 249978 AF XY: 0.0659

Gnomad AFR exome AF: 0.0286

Gnomad AMR exome AF: 0.0953

Gnomad ASJ exome AF: 0.0195

Gnomad EAS exome AF: 0.352

Gnomad FIN exome AF: 0.0331

Gnomad NFE exome AF: 0.0219

Gnomad OTH exome AF: 0.0458

GnomAD4 exome AF: 0.0387 AC: 56596 AN: 1460816 Hom.: 3291 Cov.: 32 AF XY: 0.0400 AC XY: 29065 AN XY: 726716

African (AFR) AF: 0.0279 AC: 934 AN: 33476

American (AMR) AF: 0.0898 AC: 4007 AN: 44630

Ashkenazi Jewish (ASJ) AF: 0.0174 AC: 454 AN: 26030

East Asian (EAS) AF: 0.315 AC: 12514 AN: 39694

South Asian (SAS) AF: 0.101 AC: 8668 AN: 86128

European-Finnish (FIN) AF: 0.0320 AC: 1708 AN: 53380

Middle Eastern (MID) AF: 0.0141 AC: 81 AN: 5756

European-Non Finnish (NFE) AF: 0.0228 AC: 25324 AN: 1111370

Other (OTH) AF: 0.0482 AC: 2906 AN: 60352

GnomAD4 genome AF: 0.0420 AC: 6387 AN: 152242 Hom.: 425 Cov.: 33 AF XY: 0.0463 AC XY: 3444 AN XY: 74438

African (AFR) AF: 0.0289 AC: 1201 AN: 41544

American (AMR) AF: 0.0533 AC: 815 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1746 AN: 5164

South Asian (SAS) AF: 0.113 AC: 547 AN: 4832

European-Finnish (FIN) AF: 0.0357 AC: 379 AN: 10602

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0229 AC: 1558 AN: 68028

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0275 Hom.: 233

Bravo AF: 0.0438

Asia WGS AF: 0.195 AC: 679 AN: 3478

EpiCase AF: 0.0195

EpiControl AF: 0.0189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.45
DANN	Benign	0.57
PhyloP100		-3.4
PromoterAI		-0.0088	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs964132;

hg19: chr19-19243175;

COSMIC: COSV50776784;

COSMIC: COSV50776784;