rs1953652

Variant names:

• chr1-86585518-C-T
• rs1953652
• ENST00000456587.1:n.295-14110G>A

Variant summary

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

The ENST00000456587.1(CLCA4-AS1):​n.295-14110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,828 control chromosomes in the GnomAD database, including 7,526 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 0.31 (7526 hom., cov: 32)
• Consequence: CLCA4-AS1 ENST00000456587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 7 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456587.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLCA4-AS1	NR_135837.1		n.1293-14110G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLCA4-AS1	ENST00000456587.1	TSL:3	n.295-14110G>A		intron	N/A
	CLCA4-AS1	ENST00000650379.2		n.2183-475G>A		intron	N/A
	CLCA4-AS1	ENST00000699483.1		n.1284-14110G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47638 AN: 151710 Hom.: 7521 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.314 AC: 47658 AN: 151828 Hom.: 7526 Cov.: 32 AF XY: 0.310 AC XY: 23028 AN XY: 74174

African (AFR) AF: 0.290 AC: 12000 AN: 41406

American (AMR) AF: 0.270 AC: 4119 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1401 AN: 5132

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4822

European-Finnish (FIN) AF: 0.337 AC: 3549 AN: 10526

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23314 AN: 67916

Other (OTH) AF: 0.338 AC: 712 AN: 2106

Alfa AF: 0.333 Hom.: 22512

Bravo AF: 0.310

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.51
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1953652;

hg19: chr1-87051201;