chr9-99870211-A-G

Variant names:

• chr9-99870211-A-G
• rs12686676
• ENST00000655615.1:n.178+24669T>C

Variant summary

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

The ENST00000655615.1(NAMA):​n.178+24669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,948 control chromosomes in the GnomAD database, including 16,673 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 0.45 (16673 hom., cov: 30)
• Consequence: NAMA ENST00000655615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655615.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMA	ENST00000655615.1		n.178+24669T>C		intron	N/A
	NAMA	ENST00000715777.1		n.36+24669T>C		intron	N/A
	NAMA	ENST00000725618.1		n.176+24669T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68669 AN: 151830 Hom.: 16666 Cov.: 30

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.452 AC: 68688 AN: 151948 Hom.: 16673 Cov.: 30 AF XY: 0.443 AC XY: 32905 AN XY: 74252

African (AFR) AF: 0.302 AC: 12513 AN: 41434

American (AMR) AF: 0.425 AC: 6491 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1874 AN: 3464

East Asian (EAS) AF: 0.361 AC: 1866 AN: 5166

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4812

European-Finnish (FIN) AF: 0.467 AC: 4929 AN: 10560

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37923 AN: 67940

Other (OTH) AF: 0.486 AC: 1029 AN: 2116

Alfa AF: 0.373 Hom.: 1081

Bravo AF: 0.448

Asia WGS AF: 0.324 AC: 1129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs12686676; hg19: chr9-102632493;