rs3756804

chr6-46129040-T-C

Variant summary

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

The ENST00000669498.1(ENSG00000231769):n.354+464A>G 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 0.0967 in 152,262 control chromosomes in the GnomAD database, including 830 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 0.097 (830 hom., cov: 32)
• Consequence: ENST00000669498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLIC5	NM_001370649.1	c.-55+464A>G		intron_variant
CLIC5	NM_001370650.1	c.-46+464A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669498.1	n.354+464A>G		intron_variant, non_coding_transcript_variant
	ENST00000437249.2	n.117+550A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000444038.3	n.328+464A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000689613.2	n.260+550A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14712 AN: 152144 Hom.: 829 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0967 AC: 14724 AN: 152262 Hom.: 830 Cov.: 32 AF XY: 0.0996 AC XY: 7417 AN XY: 74462

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0700 Hom.: 742

Bravo AF: 0.0950

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	9.4
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756804; hg19: chr6-46096777;