4-63092452-T-C

Position:

• chr4-63092452-T-C

Variant summary

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

The variant allele was found at a frequency of 0.597 in 151,996 control chromosomes in the GnomAD database, including 28,391 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 0.60 (28391 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63092452T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90735 AN: 151878 Hom.: 28389 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.597 AC: 90773 AN: 151996 Hom.: 28391 Cov.: 33 AF XY: 0.592 AC XY: 43958 AN XY: 74308

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.629

Alfa AF: 0.626 Hom.: 5568

Bravo AF: 0.595

Asia WGS AF: 0.431 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4349629; hg19: chr4-63958170;