ENST00000655615.1:n.178+24008T>C

Variant names:

• chr9-99870872-A-G
• rs10819699
• ENST00000655615.1:n.178+24008T>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+24008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,884 control chromosomes in the GnomAD database, including 29,446 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 0.61 (29446 hom., cov: 31)
• Consequence: NAMA ENST00000655615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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+24008T>C		intron	N/A
	NAMA	ENST00000715777.1		n.36+24008T>C		intron	N/A
	NAMA	ENST00000725618.1		n.176+24008T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93257 AN: 151766 Hom.: 29407 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.615 AC: 93348 AN: 151884 Hom.: 29446 Cov.: 31 AF XY: 0.605 AC XY: 44915 AN XY: 74190

African (AFR) AF: 0.537 AC: 22237 AN: 41436

American (AMR) AF: 0.641 AC: 9759 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1886 AN: 5148

South Asian (SAS) AF: 0.367 AC: 1766 AN: 4812

European-Finnish (FIN) AF: 0.599 AC: 6309 AN: 10538

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46926 AN: 67948

Other (OTH) AF: 0.639 AC: 1348 AN: 2108

Alfa AF: 0.661 Hom.: 15515

Bravo AF: 0.619

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10819699; hg19: chr9-102633154;