rs11960458

Variant names:

• chr5-151100959-C-A
• rs11960458
• NM_001155.5:c.*489G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-151100959-C-A
• chr5-151100959-C-T

Variant summary

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

The NM_001155.5(ANXA6):​c.*489G>T variant causes a 3 prime UTR 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: ANXA6 NM_001155.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 23 publications found

Genes affected

ANXA6 (HGNC:544): (annexin A6) Annexin VI belongs to a family of calcium-dependent membrane and phospholipid binding proteins. Several members of the annexin family have been implicated in membrane-related events along exocytotic and endocytotic pathways. The annexin VI gene is approximately 60 kbp long and contains 26 exons. It encodes a protein of about 68 kDa that consists of eight 68-amino acid repeats separated by linking sequences of variable lengths. It is highly similar to human annexins I and II sequences, each of which contain four such repeats. Annexin VI has been implicated in mediating the endosome aggregation and vesicle fusion in secreting epithelia during exocytosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2010]

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=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA6	NM_001155.5	c.*489G>T		3_prime_UTR_variant	Exon 26 of 26	ENST00000354546.10	NP_001146.2
ANXA6	NM_001363114.2	c.*489G>T		3_prime_UTR_variant	Exon 25 of 25		NP_001350043.1
ANXA6	NM_001193544.2	c.*489G>T		3_prime_UTR_variant	Exon 25 of 25		NP_001180473.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA6	ENST00000354546.10	c.*489G>T		3_prime_UTR_variant	Exon 26 of 26	1	NM_001155.5	ENSP00000346550.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 304630 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 173406

African (AFR) AF: 0.00 AC: 0 AN: 8654

American (AMR) AF: 0.00 AC: 0 AN: 27298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10816

East Asian (EAS) AF: 0.00 AC: 0 AN: 9242

South Asian (SAS) AF: 0.00 AC: 0 AN: 59746

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2784

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 159430

Other (OTH) AF: 0.00 AC: 0 AN: 14270

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 9215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.3
DANN	Benign	0.97
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs11960458; hg19: chr5-150480520;