chr12-9232829-C-T

Variant names:

• chr12-9232829-C-T
• rs34362
• ENST00000543404.5:n.381-249G>A

Variant summary

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

The NR_040112.1(A2MP1):​n.381-249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,056 control chromosomes in the GnomAD database, including 9,512 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 0.34 (9512 hom., cov: 32)
• Consequence: A2MP1 NR_040112.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 3 publications found

Genes affected

A2MP1 (HGNC:):

LINC00987 (HGNC:48911): (long intergenic non-protein coding RNA 987)

A2MP1 (HGNC:8): (alpha-2-macroglobulin pseudogene 1)

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 = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_040112.1. 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
	A2MP1	NR_040112.1		n.381-249G>A		intron	N/A
	A2MP1	NR_199634.1		n.3169-249G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	A2MP1	ENST00000543404.5	TSL:5	n.381-249G>A		intron	N/A
	A2MP1	ENST00000566278.6	TSL:6	n.3480-249G>A		intron	N/A
	LINC00987	ENST00000838855.1		n.99-13640C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51358 AN: 151938 Hom.: 9484 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.338 AC: 51431 AN: 152056 Hom.: 9512 Cov.: 32 AF XY: 0.335 AC XY: 24904 AN XY: 74322

African (AFR) AF: 0.501 AC: 20771 AN: 41458

American (AMR) AF: 0.253 AC: 3859 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.142 AC: 739 AN: 5190

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4816

European-Finnish (FIN) AF: 0.290 AC: 3067 AN: 10578

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19477 AN: 67956

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.210 Hom.: 503

Bravo AF: 0.338

Asia WGS AF: 0.246 AC: 856 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs34362; hg19: chr12-9385425;