rs12551906

Variant names:

• chr9-99356808-G-A
• rs12551906
• ENST00000604237.5:n.200-1206C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000603491.2(NAMA):​n.321C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,122 control chromosomes in the GnomAD database, including 4,150 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 0.21 (4150 hom., cov: 31)
• Consequence: NAMA ENST00000603491.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 12 publications found

Genes affected

NAMA (HGNC:42408): (non-protein coding RNA, associated with MAP kinase pathway and growth arrest)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603491.2. 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
	NAMA	NR_102270.1		n.1971-1206C>T		intron	N/A
	NAMA	NR_102271.1		n.1419-1206C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMA	ENST00000604237.5	TSL:1	n.200-1206C>T		intron	N/A
	NAMA	ENST00000604258.6	TSL:1	n.2019-1206C>T		intron	N/A
	NAMA	ENST00000603491.2	TSL:6	n.321C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31662 AN: 152004 Hom.: 4152 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.208 AC: 31651 AN: 152122 Hom.: 4150 Cov.: 31 AF XY: 0.209 AC XY: 15556 AN XY: 74346

African (AFR) AF: 0.0744 AC: 3091 AN: 41542

American (AMR) AF: 0.185 AC: 2833 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3472

East Asian (EAS) AF: 0.0921 AC: 477 AN: 5180

South Asian (SAS) AF: 0.283 AC: 1357 AN: 4802

European-Finnish (FIN) AF: 0.295 AC: 3110 AN: 10552

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19367 AN: 67980

Other (OTH) AF: 0.195 AC: 411 AN: 2110

Alfa AF: 0.256 Hom.: 9722

Bravo AF: 0.191

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		0.14

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: rs12551906;

hg19: chr9-102119090;