4-54088264-G-A

Position:

• chr4-54088264-G-A

Variant summary

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

The XM_047450063.1(CHIC2):​c.-1494+3517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,810 control chromosomes in the GnomAD database, including 14,256 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 0.42 (14256 hom., cov: 31)
• Consequence: CHIC2 XM_047450063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

Genes affected

CHIC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHIC2	XM_047450063.1	c.-1494+3517C>T		intron_variant			XP_047306019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63035 AN: 151692 Hom.: 14218 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.416 AC: 63133 AN: 151810 Hom.: 14256 Cov.: 31 AF XY: 0.407 AC XY: 30226 AN XY: 74182

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.405

Alfa AF: 0.394 Hom.: 1981

Bravo AF: 0.421

Asia WGS AF: 0.290 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.6
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs714861; hg19: chr4-54954431; COSMIC: COSV72264526; COSMIC: COSV72264526;