rs35775808

Variant names:

• chr9-99463262-A-G
• rs35775808
• ENST00000652827.1:n.231-190T>C

Variant summary

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

The ENST00000652827.1(NAMA):​n.231-190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 152,302 control chromosomes in the GnomAD database, including 212 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 0.045 (212 hom., cov: 32)
• Consequence: NAMA ENST00000652827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652827.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMA	ENST00000652827.1		n.231-190T>C		intron	N/A
	NAMA	ENST00000655615.1		n.269-190T>C		intron	N/A
	NAMA	ENST00000715772.1		n.281-63614T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6785 AN: 152184 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0445 AC: 6784 AN: 152302 Hom.: 212 Cov.: 32 AF XY: 0.0450 AC XY: 3348 AN XY: 74470

African (AFR) AF: 0.0125 AC: 520 AN: 41578

American (AMR) AF: 0.0387 AC: 593 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0355 AC: 171 AN: 4820

European-Finnish (FIN) AF: 0.0731 AC: 776 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4399 AN: 68012

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0443 Hom.: 114

Bravo AF: 0.0410

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.71
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs35775808; hg19: chr9-102225544;