9-99377245-T-C

Position:

• chr9-99377245-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 9-99377245-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,980 control chromosomes in the GnomAD database, including 30,225 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 0.62 (30212 hom., cov: 31)
  • Exomes 𝑓: 0.71 (13 hom.)
• Consequence: NAMA ENST00000605043.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAMA	ENST00000605043.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93795 AN: 151822 Hom.: 30213 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.643

GnomAD4 exome AF: 0.714 AC: 30 AN: 42 Hom.: 13 Cov.: 0 AF XY: 0.714 AC XY: 20 AN XY: 28

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.617 AC: 93817 AN: 151938 Hom.: 30212 Cov.: 31 AF XY: 0.612 AC XY: 45466 AN XY: 74288

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.637

Alfa AF: 0.705 Hom.: 74325

Bravo AF: 0.602

Asia WGS AF: 0.433 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491654; hg19: chr9-102139527;