rs16918212

Variant names:

• chr12-9232362-C-A
• rs16918212
• ENST00000543404.5:n.599G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-9232362-C-A
• chr12-9232362-C-G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000543404.5(A2MP1):​n.599G>T variant causes a splice region, non coding transcript exon change. The variant allele was found at a frequency of 0.124 in 152,548 control chromosomes in the GnomAD database, including 1,359 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 0.12 (1356 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3 hom.)
• Consequence: A2MP1 ENST00000543404.5 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.73
• Publications: 7 publications found

Genes affected

A2MP1 (HGNC:):

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

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

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543404.5. 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
	A2MP1	NR_040112.1		n.599G>T		splice_region non_coding_transcript_exon	Exon 3 of 9
	A2MP1	NR_199634.1		n.3387G>T		splice_region non_coding_transcript_exon	Exon 24 of 30

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	A2MP1	ENST00000543404.5	TSL:5	n.599G>T		splice_region non_coding_transcript_exon	Exon 3 of 9
	A2MP1	ENST00000566278.6	TSL:6	n.3698G>T		splice_region non_coding_transcript_exon	Exon 27 of 32
	LINC00987	ENST00000838855.1		n.99-14107C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18865 AN: 151998 Hom.: 1353 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.116 AC: 50 AN: 432 Hom.: 3 Cov.: 0 AF XY: 0.124 AC XY: 32 AN XY: 258

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.121 AC: 48 AN: 396

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 2 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.124 AC: 18904 AN: 152116 Hom.: 1356 Cov.: 32 AF XY: 0.121 AC XY: 9030 AN XY: 74364

African (AFR) AF: 0.199 AC: 8243 AN: 41460

American (AMR) AF: 0.102 AC: 1559 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3468

East Asian (EAS) AF: 0.0239 AC: 124 AN: 5190

South Asian (SAS) AF: 0.0859 AC: 415 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1065 AN: 10562

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6940 AN: 67994

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.108 Hom.: 3804

Bravo AF: 0.129

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	16
DANN	Benign	0.81
PhyloP100		5.7

Splicing

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

Other links and lift over

dbSNP: rs16918212; hg19: chr12-9384958;