rs1517899

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CLCA3P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CLCA3P	NR_024604.1	n.576-683T>C		intron_variant
CLCA4-AS1	NR_135837.1	n.1292+54988A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLCA3P	ENST00000466454.1	n.576-683T>C		intron_variant		1
CLCA3P	ENST00000284054.7	n.579-683T>C		intron_variant		5
CLCA4-AS1	ENST00000456587.1	n.294+9762A>G		intron_variant		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

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.422

Alfa AF: 0.313 Hom.: 1076

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517899; hg19: chr1-87103858;