5-63737891-A-G

Position:

• chr5-63737891-A-G

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 0.202 in 152,052 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30682 AN: 151934 Hom.: 3307 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.202 AC: 30695 AN: 152052 Hom.: 3308 Cov.: 33 AF XY: 0.197 AC XY: 14670 AN XY: 74344

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0227

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.203

Alfa AF: 0.208 Hom.: 648

Bravo AF: 0.207

Asia WGS AF: 0.0720 AC: 253 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10042968; hg19: chr5-63033718;