rs2292734

Positions:

• chr4-168164442-C-T

Variant summary

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

The NM_007193.5(ANXA10):​c.400+154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,958 control chromosomes in the GnomAD database, including 27,172 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 0.59 (27172 hom., cov: 32)
• Consequence: ANXA10 NM_007193.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

ANXA10 (HGNC:534): (annexin A10) This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. The function of this gene has not yet been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA10	NM_007193.5	c.400+154C>T		intron_variant		ENST00000359299.8	NP_009124.2
ANXA10	XM_011531571.3	c.460+154C>T		intron_variant			XP_011529873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA10	ENST00000359299.8	c.400+154C>T		intron_variant		1	NM_007193.5	ENSP00000352248	P1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89278 AN: 151840 Hom.: 27155 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.588 AC: 89340 AN: 151958 Hom.: 27172 Cov.: 32 AF XY: 0.577 AC XY: 42816 AN XY: 74246

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.590

Alfa AF: 0.579 Hom.: 3238

Bravo AF: 0.597

Asia WGS AF: 0.398 AC: 1382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2292734; hg19: chr4-169085593;