rs1425118

Variant names:

• chr2-216094176-C-G
• rs1425118
• NM_001142311.2:c.-126-1662C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-216094176-C-G
• chr2-216094176-C-T

Variant summary

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

The NM_001142311.2(TMEM169):​c.-126-1662C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,018 control chromosomes in the GnomAD database, including 2,935 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 0.19 (2935 hom., cov: 32)
• Consequence: TMEM169 NM_001142311.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 4 publications found

Genes affected

TMEM169 (HGNC:25130): (transmembrane protein 169) 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM169	NM_001142311.2	c.-126-1662C>G		intron_variant	Intron 1 of 2	ENST00000437356.7	NP_001135783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM169	ENST00000437356.7	c.-126-1662C>G		intron_variant	Intron 1 of 2	1	NM_001142311.2	ENSP00000401305.2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29484 AN: 151900 Hom.: 2935 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.194 AC: 29498 AN: 152018 Hom.: 2935 Cov.: 32 AF XY: 0.193 AC XY: 14345 AN XY: 74306

African (AFR) AF: 0.181 AC: 7486 AN: 41422

American (AMR) AF: 0.180 AC: 2741 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.119 AC: 613 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1525 AN: 10562

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14307 AN: 68000

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.0970 Hom.: 150

Bravo AF: 0.192

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.36
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: rs1425118; hg19: chr2-216958899;