rs4743348

Variant names:

• chr9-99413775-C-T
• rs4743348
• ENST00000652827.1:n.378-14127G>A

Variant summary

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

The ENST00000652827.1(NAMA):​n.378-14127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,056 control chromosomes in the GnomAD database, including 8,748 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 0.33 (8748 hom., cov: 32)
• Consequence: NAMA ENST00000652827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 publications found

Genes affected

NAMA (HGNC:42408): (non-protein coding RNA, associated with MAP kinase pathway and growth arrest)

LOC107987011 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 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.378-14127G>A		intron	N/A
	NAMA	ENST00000655615.1		n.310-14127G>A		intron	N/A
	NAMA	ENST00000715772.1		n.281-14127G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50732 AN: 151938 Hom.: 8744 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.334 AC: 50759 AN: 152056 Hom.: 8748 Cov.: 32 AF XY: 0.329 AC XY: 24488 AN XY: 74330

African (AFR) AF: 0.331 AC: 13729 AN: 41464

American (AMR) AF: 0.383 AC: 5843 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1422 AN: 5178

South Asian (SAS) AF: 0.281 AC: 1355 AN: 4818

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10578

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22936 AN: 67964

Other (OTH) AF: 0.379 AC: 801 AN: 2112

Alfa AF: 0.330 Hom.: 1070

Bravo AF: 0.350

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.76
DANN	Benign	0.58
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4743348; hg19: chr9-102176057; COSMIC: COSV60381835;