rs17804080

Positions:

• chr12-9235414-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000566278.6(A2MP1):​n.2848-166G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
A2MP1	ENST00000566278.6	n.2848-166G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0950 Hom.: 307

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17804080; hg19: chr12-9388010;