1-211654792-A-G

Variant names:

• chr1-211654792-A-G
• rs7516189
• ENST00000412871.1:n.*211A>G

Variant summary

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

The ENST00000412871.1(NTRAS):​n.*211A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,986 control chromosomes in the GnomAD database, including 11,437 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 0.37 (11437 hom., cov: 32)
• Consequence: NTRAS ENST00000412871.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 6 publications found

Genes affected

NTRAS (HGNC:52478): (non-coding transcript regulating alternative splicing)

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 (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412871.1. 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
	NTRAS	NR_131925.1		n.*170A>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTRAS	ENST00000412871.1	TSL:2	n.*211A>G		downstream_gene	N/A
	NTRAS	ENST00000430123.2	TSL:3	n.*168A>G		downstream_gene	N/A
	NTRAS	ENST00000653761.1		n.*170A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56808 AN: 151868 Hom.: 11432 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.374 AC: 56842 AN: 151986 Hom.: 11437 Cov.: 32 AF XY: 0.367 AC XY: 27285 AN XY: 74286

African (AFR) AF: 0.305 AC: 12633 AN: 41462

American (AMR) AF: 0.299 AC: 4559 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3472

East Asian (EAS) AF: 0.0392 AC: 202 AN: 5152

South Asian (SAS) AF: 0.284 AC: 1366 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4110 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31419 AN: 67946

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.429 Hom.: 66610

Bravo AF: 0.365

Asia WGS AF: 0.175 AC: 610 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	3.5
DANN	Benign	0.49
PhyloP100		0.47

Splicing

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: rs7516189;

hg19: chr1-211828134;