rs12551906

chr9-99356808-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_102271.1(NAMA):n.1419-1206C>T variant causes a intron, non coding transcript 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 NR_102271.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAMA	NR_102271.1	n.1419-1206C>T		intron_variant, non_coding_transcript_variant
NAMA	NR_102270.1	n.1971-1206C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAMA	ENST00000604237.5	n.200-1206C>T		intron_variant, non_coding_transcript_variant		1
NAMA	ENST00000604258.5	n.1941-1206C>T		intron_variant, non_coding_transcript_variant		1
NAMA	ENST00000605377.5	n.244-1206C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0921

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.195

Alfa AF: 0.265 Hom.: 7395

Bravo AF: 0.191

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
Cadd	Benign	15
Dann	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12551906; hg19: chr9-102119090;