rs7047636

Variant names:

• chr9-99817185-C-G
• rs7047636
• ENST00000427039.1:n.69+2636G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-99817185-C-G
• chr9-99817185-C-T

Variant summary

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

The ENST00000427039.1(NAMA):​n.69+2636G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,942 control chromosomes in the GnomAD database, including 10,116 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 0.36 (10116 hom., cov: 32)
• Consequence: NAMA ENST00000427039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 3 publications found

Genes affected

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

LOC101928438 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928438	NR_109802.1	n.69+2636G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAMA	ENST00000427039.1	n.69+2636G>C		intron_variant	Intron 1 of 6	2
NAMA	ENST00000652827.1	n.101+2636G>C		intron_variant	Intron 1 of 5
NAMA	ENST00000655615.1	n.268+21801G>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54485 AN: 151824 Hom.: 10097 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.359 AC: 54547 AN: 151942 Hom.: 10116 Cov.: 32 AF XY: 0.350 AC XY: 26024 AN XY: 74268

African (AFR) AF: 0.420 AC: 17404 AN: 41420

American (AMR) AF: 0.284 AC: 4337 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3470

East Asian (EAS) AF: 0.174 AC: 901 AN: 5182

South Asian (SAS) AF: 0.187 AC: 900 AN: 4814

European-Finnish (FIN) AF: 0.328 AC: 3452 AN: 10518

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24915 AN: 67950

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.363 Hom.: 1214

Bravo AF: 0.362

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.55
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7047636; hg19: chr9-102579467;