rs649057

Variant names:

• chr9-99472041-C-A
• rs649057
• ENST00000652827.1:n.231-8969G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-99472041-C-A
• chr9-99472041-C-G
• chr9-99472041-C-T

Variant summary

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

The ENST00000652827.1(NAMA):​n.231-8969G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,278 control chromosomes in the GnomAD database, including 760 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 0.083 (760 hom., cov: 32)
• Consequence: NAMA ENST00000652827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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.231-8969G>T		intron	N/A
	NAMA	ENST00000655615.1		n.269-8969G>T		intron	N/A
	NAMA	ENST00000715772.1		n.281-72393G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12628 AN: 152160 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0834 AC: 12699 AN: 152278 Hom.: 760 Cov.: 32 AF XY: 0.0845 AC XY: 6290 AN XY: 74476

African (AFR) AF: 0.110 AC: 4581 AN: 41542

American (AMR) AF: 0.179 AC: 2732 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3466

East Asian (EAS) AF: 0.145 AC: 752 AN: 5190

South Asian (SAS) AF: 0.0897 AC: 433 AN: 4826

European-Finnish (FIN) AF: 0.0139 AC: 148 AN: 10626

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0505 AC: 3432 AN: 68012

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0683 Hom.: 1410

Bravo AF: 0.102

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.25
PhyloP100		-0.063

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: rs649057;

hg19: chr9-102234323;