XM_011511267.3:c.2444+8754G>A

Variant names:

• chr2-241227135-G-A
• rs1677
• XM_011511267.3:c.2444+8754G>A

Variant summary

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

The XM_011511267.3(ANO7):​c.2444+8754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,264 control chromosomes in the GnomAD database, including 42,097 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 0.73 (42042 hom., cov: 31)
  • Exomes 𝑓: 0.84 (55 hom.)
• Consequence: ANO7 XM_011511267.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09

Genes affected

ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]

LOC105376810 (HGNC:):

HDLBP (HGNC:4857): (high density lipoprotein binding protein) The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HDLBP	NM_005336.6	c.*2466C>T		downstream_gene_variant		ENST00000310931.10	NP_005327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931.10	c.*2466C>T		downstream_gene_variant		1	NM_005336.6	ENSP00000312042.4
HDLBP	ENST00000391975.5	c.*2466C>T		downstream_gene_variant		1		ENSP00000375836.1
HDLBP	ENST00000427183.6	c.*2466C>T		downstream_gene_variant		2		ENSP00000399139.2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111316 AN: 151988 Hom.: 42007 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.780

GnomAD4 exome AF: 0.835 AC: 132 AN: 158 Hom.: 55 AF XY: 0.854 AC XY: 82 AN XY: 96

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.856

Gnomad4 NFE exome AF: 0.793

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.732 AC: 111403 AN: 152106 Hom.: 42042 Cov.: 31 AF XY: 0.740 AC XY: 54993 AN XY: 74356

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.783

Alfa AF: 0.790 Hom.: 45900

Bravo AF: 0.729

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.026
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1677; hg19: chr2-242166550;