9-99367140-T-G

Variant names:

• chr9-99367140-T-G
• rs1555573
• ENST00000604258.6:n.1458+521A>C

Variant summary

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

The ENST00000725668.1(NAMA):​n.664A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,094 control chromosomes in the GnomAD database, including 11,182 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 0.37 (11182 hom., cov: 33)
• Consequence: NAMA ENST00000725668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725668.1. 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
	NAMA	NR_102270.1		n.1410+521A>C		intron	N/A
	NAMA	NR_102271.1		n.1273+521A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMA	ENST00000604258.6	TSL:1	n.1458+521A>C		intron	N/A
	NAMA	ENST00000605707.1	TSL:1	n.1648+521A>C		intron	N/A
	NAMA	ENST00000725668.1		n.664A>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56074 AN: 151976 Hom.: 11161 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.369 AC: 56144 AN: 152094 Hom.: 11182 Cov.: 33 AF XY: 0.375 AC XY: 27891 AN XY: 74388

African (AFR) AF: 0.457 AC: 18939 AN: 41456

American (AMR) AF: 0.457 AC: 6992 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3351 AN: 5180

South Asian (SAS) AF: 0.393 AC: 1889 AN: 4808

European-Finnish (FIN) AF: 0.382 AC: 4044 AN: 10578

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18959 AN: 67988

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.335 Hom.: 1199

Bravo AF: 0.382

Asia WGS AF: 0.579 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.47
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs1555573; hg19: chr9-102129422;