5-63744946-A-G

Position:

• chr5-63744946-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 0.493 in 151,890 control chromosomes in the GnomAD database, including 19,300 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 0.49 (19300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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: 0.493 AC: 74794 AN: 151772 Hom.: 19288 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.493 AC: 74834 AN: 151890 Hom.: 19300 Cov.: 32 AF XY: 0.502 AC XY: 37230 AN XY: 74222

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.508

Alfa AF: 0.482 Hom.: 2174

Bravo AF: 0.480

Asia WGS AF: 0.738 AC: 2563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
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: rs7736910; hg19: chr5-63040773;