5-163862989-G-A

Position:

• chr5-163862989-G-A

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 0.654 in 151,270 control chromosomes in the GnomAD database, including 32,485 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 0.65 (32485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.654 AC: 98900 AN: 151154 Hom.: 32487 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.654 AC: 98928 AN: 151270 Hom.: 32485 Cov.: 31 AF XY: 0.649 AC XY: 47965 AN XY: 73850

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.671

Alfa AF: 0.638 Hom.: 3714

Bravo AF: 0.671

Asia WGS AF: 0.633 AC: 2198 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.36
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs391763; hg19: chr5-163289995;