rs1227236

Variant names:

• chr10-64826548-A-C
• rs1227236
• ENST00000404883.2:n.977A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-64826548-A-C
• chr10-64826548-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000404883.2(ANXA2P3):​n.977A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANXA2P3 ENST00000404883.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• Publications: 5 publications found

Genes affected

ANXA2P3 (HGNC:540): (annexin A2 pseudogene 3)

ENSG00000293732 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA2P3	NR_001446.2	n.1021A>C		non_coding_transcript_exon_variant	Exon 1 of 1
LOC105378336	XR_946020.2	n.49+11546A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA2P3	ENST00000404883.2	n.977A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293732	ENST00000718642.1	n.195+11546A>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 575324 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 315622

African (AFR) AF: 0.00 AC: 0 AN: 16390

American (AMR) AF: 0.00 AC: 0 AN: 41800

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19246

East Asian (EAS) AF: 0.00 AC: 0 AN: 32926

South Asian (SAS) AF: 0.00 AC: 0 AN: 68854

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42060

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3908

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 320444

Other (OTH) AF: 0.00 AC: 0 AN: 29696

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.1
DANN	Benign	0.35
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1227236; hg19: chr10-66586305;