rs1953652

chr1-86585518-C-T

Variant summary

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

The NR_135837.1(CLCA4-AS1):n.1293-14110G>A variant causes a intron, non coding transcript 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 NR_135837.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

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

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 (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLCA4-AS1	NR_135837.1	n.1293-14110G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLCA4-AS1	ENST00000699483.1	n.1284-14110G>A		intron_variant, non_coding_transcript_variant
CLCA4-AS1	ENST00000456587.1	n.295-14110G>A		intron_variant, non_coding_transcript_variant		3
CLCA4-AS1	ENST00000650379.1	n.2183-475G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.338

Alfa AF: 0.337 Hom.: 8872

Bravo AF: 0.310

Asia WGS AF: 0.245 AC: 850 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	0.98
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953652; hg19: chr1-87051201;