12-1529005-A-G

Variant names:

• chr12-1529005-A-G
• rs2887571
• NR_160736.1:n.2854T>C

Variant summary

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

The NR_160736.1(LOC107984507):​n.2854T>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 0.223 in 152,066 control chromosomes in the GnomAD database, including 3,925 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 0.22 (3925 hom., cov: 32)
• Consequence: LOC107984507 NR_160736.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 36 publications found

Genes affected

LOC107984507 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_160736.1. 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
	LOC107984507	NR_160736.1		n.2854T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33899 AN: 151948 Hom.: 3924 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.223 AC: 33925 AN: 152066 Hom.: 3925 Cov.: 32 AF XY: 0.222 AC XY: 16470 AN XY: 74326

African (AFR) AF: 0.192 AC: 7949 AN: 41482

American (AMR) AF: 0.204 AC: 3119 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.157 AC: 809 AN: 5154

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4808

European-Finnish (FIN) AF: 0.191 AC: 2020 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17058 AN: 67970

Other (OTH) AF: 0.215 AC: 455 AN: 2116

Alfa AF: 0.241 Hom.: 11953

Bravo AF: 0.217

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2887571; hg19: chr12-1638171;