1-86548977-G-A

Variant names:

• chr1-86548977-G-A
• rs1543467
• NM_012128.4:c.159+1699G>A

Variant summary

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

The NM_012128.4(CLCA4):​c.159+1699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,014 control chromosomes in the GnomAD database, including 21,379 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 0.48 (21379 hom., cov: 32)
• Consequence: CLCA4 NM_012128.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 4 publications found

Genes affected

CLCA4 (HGNC:2018): (chloride channel accessory 4) The protein encoded by this gene belongs 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. Alternative splicing results in multiple transcript variants, only one of which is thought to be protein coding. [provided by RefSeq, Dec 2008]

CLCA4 Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012128.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLCA4	NM_012128.4	MANE Select	c.159+1699G>A		intron	N/A	NP_036260.2
	CLCA4	NR_024602.2		n.201+1699G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLCA4	ENST00000370563.3	TSL:1 MANE Select	c.159+1699G>A		intron	N/A	ENSP00000359594.3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72288 AN: 151896 Hom.: 21326 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.476 AC: 72392 AN: 152014 Hom.: 21379 Cov.: 32 AF XY: 0.477 AC XY: 35431 AN XY: 74332

African (AFR) AF: 0.824 AC: 34150 AN: 41462

American (AMR) AF: 0.319 AC: 4878 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3862 AN: 5162

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4820

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10546

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21200 AN: 67962

Other (OTH) AF: 0.452 AC: 956 AN: 2116

Alfa AF: 0.362 Hom.: 5705

Bravo AF: 0.491

Asia WGS AF: 0.633 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1543467; hg19: chr1-87014660;