rs1002841

Variant names:

• chr9-99379711-T-C
• rs1002841
• ENST00000715772.1:n.507+11045A>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+11045A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,064 control chromosomes in the GnomAD database, including 9,833 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 0.35 (9833 hom., cov: 32)
• Consequence: NAMA ENST00000715772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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

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	ENST00000715772.1		n.507+11045A>G		intron	N/A
	NAMA	ENST00000725614.1		n.400+19828A>G		intron	N/A
	NAMA	ENST00000725645.1		n.110+19828A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52994 AN: 151946 Hom.: 9825 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.349 AC: 53036 AN: 152064 Hom.: 9833 Cov.: 32 AF XY: 0.343 AC XY: 25467 AN XY: 74342

African (AFR) AF: 0.475 AC: 19677 AN: 41468

American (AMR) AF: 0.293 AC: 4472 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1406 AN: 3464

East Asian (EAS) AF: 0.264 AC: 1368 AN: 5176

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2330 AN: 10570

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21097 AN: 67968

Other (OTH) AF: 0.382 AC: 807 AN: 2112

Alfa AF: 0.326 Hom.: 1411

Bravo AF: 0.361

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.66
PhyloP100		0.010

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1002841;

hg19: chr9-102141993;

COSMIC: COSV74095194;