chr9-99377245-T-C

Variant names:

• chr9-99377245-T-C
• rs10491654
• ENST00000715772.1:n.507+13511A>G

Variant summary

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

The ENST00000715772.1(NAMA):​n.507+13511A>G variant causes a intron 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 ENST00000715772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 8 publications found

Genes affected

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

ENSG00000287955 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715772.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMA	ENST00000715772.1		n.507+13511A>G		intron	N/A
	NAMA	ENST00000725614.1		n.401-21663A>G		intron	N/A
	NAMA	ENST00000725645.1		n.111-21643A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.750 AC: 18 AN: 24

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.479 AC: 19835 AN: 41398

American (AMR) AF: 0.538 AC: 8214 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1834 AN: 5156

South Asian (SAS) AF: 0.643 AC: 3092 AN: 4810

European-Finnish (FIN) AF: 0.618 AC: 6521 AN: 10554

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49504 AN: 67956

Other (OTH) AF: 0.637 AC: 1342 AN: 2108

Alfa AF: 0.691 Hom.: 97116

Bravo AF: 0.602

Asia WGS AF: 0.433 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10491654; hg19: chr9-102139527;