rs1517899

Variant names:

• chr1-86638175-T-C
• rs1517899
• ENST00000466454.1:n.576-683T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-86638175-T-C
• chr1-86638175-T-G

Variant summary

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

The ENST00000466454.1(CLCA3P):​n.576-683T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,924 control chromosomes in the GnomAD database, including 12,615 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 0.40 (12615 hom., cov: 32)
• Consequence: CLCA3P ENST00000466454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 2 publications found

Genes affected

CLCA3P (HGNC:):

CLCA4-AS1 (HGNC:54055): (CLCA4 antisense RNA 1)

CLCA3P (HGNC:2017): (chloride channel accessory 3, pseudogene) This gene is a transcribed pseudogene belonging to the calcium sensitive chloride conductance protein family. To date, all members of this gene family map to the same site on chromosome 1p31-p22 and share high degrees of homology in size, sequence and predicted structure, but differ significantly in their tissue distributions. This gene contains several nonsense codons compared to other family members that render the transcript a candidate for nonsense-mediated mRNA decay (NMD). Therefore, this gene is unlikely to be protein-coding. [provided by RefSeq, Jan 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLCA3P	NR_024604.1	n.576-683T>C		intron_variant	Intron 4 of 14
CLCA4-AS1	NR_135837.1	n.1292+54988A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLCA3P	ENST00000466454.1	n.576-683T>C		intron_variant	Intron 4 of 14	1
CLCA3P	ENST00000284054.7	n.579-683T>C		intron_variant	Intron 4 of 13	5
CLCA4-AS1	ENST00000456587.1	n.294+9762A>G		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61338 AN: 151804 Hom.: 12606 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.404 AC: 61389 AN: 151924 Hom.: 12615 Cov.: 32 AF XY: 0.393 AC XY: 29206 AN XY: 74228

African (AFR) AF: 0.470 AC: 19480 AN: 41432

American (AMR) AF: 0.386 AC: 5882 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2175 AN: 5160

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3122 AN: 10560

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26781 AN: 67948

Other (OTH) AF: 0.422 AC: 890 AN: 2108

Alfa AF: 0.319 Hom.: 1152

Bravo AF: 0.422

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1517899; hg19: chr1-87103858;