rs17804080

Variant names:

• chr12-9235414-C-T
• rs17804080
• ENST00000566278.6:n.2848-166G>A

Variant summary

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

The ENST00000566278.6(A2MP1):​n.2848-166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 152,216 control chromosomes in the GnomAD database, including 601 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 0.083 (601 hom., cov: 32)
• Consequence: A2MP1 ENST00000566278.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
A2MP1	NR_199634.1	n.2683+851G>A		intron_variant	Intron 21 of 29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
A2MP1	ENST00000566278.6	n.2848-166G>A		intron_variant	Intron 22 of 31	6
LINC00987	ENST00000838855.1	n.99-11055C>T		intron_variant	Intron 1 of 5
LINC00987	ENST00000838856.1	n.144-11055C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12559 AN: 152098 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.0555

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0826 AC: 12567 AN: 152216 Hom.: 601 Cov.: 32 AF XY: 0.0816 AC XY: 6076 AN XY: 74418

African (AFR) AF: 0.0555 AC: 2304 AN: 41548

American (AMR) AF: 0.0859 AC: 1314 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3468

East Asian (EAS) AF: 0.0235 AC: 122 AN: 5190

South Asian (SAS) AF: 0.0848 AC: 409 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6898 AN: 67994

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0950 Hom.: 342

Bravo AF: 0.0798

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17804080; hg19: chr12-9388010;