5-63998870-A-C

Position:

• chr5-63998870-A-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 0.588 in 152,014 control chromosomes in the GnomAD database, including 27,021 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 0.59 (27021 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63998870A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89265 AN: 151896 Hom.: 26983 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.588 AC: 89354 AN: 152014 Hom.: 27021 Cov.: 32 AF XY: 0.586 AC XY: 43518 AN XY: 74290

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.594

Alfa AF: 0.528 Hom.: 16848

Bravo AF: 0.605

Asia WGS AF: 0.682 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs382098; hg19: chr5-63294697;