rs4970988

Variant names:

• chr1-150977586-G-A
• rs4970988
• ENST00000808151.1:n.594G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-150977586-G-A
• chr1-150977586-G-T

Variant summary

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

The ENST00000808151.1(ENSG00000231073):​n.594G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,150 control chromosomes in the GnomAD database, including 8,435 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 0.31 (8435 hom., cov: 32)
• Consequence: ENSG00000231073 ENST00000808151.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 27 publications found

Genes affected

ENSG00000231073 (HGNC:):

ANXA9 (HGNC:547): (annexin A9) The annexins are a family of calcium-dependent phospholipid-binding proteins. Members of the annexin family contain 4 internal repeat domains, each of which includes a type II calcium-binding site. The calcium-binding sites are required for annexins to aggregate and cooperatively bind anionic phospholipids and extracellular matrix proteins. This gene encodes a divergent member of the annexin protein family in which all four homologous type II calcium-binding sites in the conserved tetrad core contain amino acid substitutions that ablate their function. However, structural analysis suggests that the conserved putative ion channel formed by the tetrad core is intact. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA9	XM_047431989.1	c.-2352G>A		5_prime_UTR_variant	Exon 1 of 15		XP_047287945.1
ANXA9	XM_047431991.1	c.-2513G>A		upstream_gene_variant			XP_047287947.1
ANXA9	XM_047431997.1	c.-2448G>A		upstream_gene_variant			XP_047287953.1
ANXA9	XM_047431999.1	c.-2352G>A		upstream_gene_variant			XP_047287955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231073	ENST00000808151.1	n.594G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000231073	ENST00000808152.1	n.69G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46752 AN: 152032 Hom.: 8430 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.307 AC: 46760 AN: 152150 Hom.: 8435 Cov.: 32 AF XY: 0.315 AC XY: 23454 AN XY: 74364

African (AFR) AF: 0.119 AC: 4933 AN: 41530

American (AMR) AF: 0.467 AC: 7139 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2084 AN: 5158

South Asian (SAS) AF: 0.504 AC: 2431 AN: 4828

European-Finnish (FIN) AF: 0.344 AC: 3644 AN: 10578

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24078 AN: 67986

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.327 Hom.: 14644

Bravo AF: 0.307

Asia WGS AF: 0.412 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.43
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs4970988; hg19: chr1-150950062;