5-168532302-C-G

Variant names:

• chr5-168532302-C-G
• rs244895

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 0.695 in 152,094 control chromosomes in the GnomAD database, including 37,301 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 0.70 (37301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105637 AN: 151976 Hom.: 37251 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.695 AC: 105743 AN: 152094 Hom.: 37301 Cov.: 33 AF XY: 0.697 AC XY: 51848 AN XY: 74340

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.672

Alfa AF: 0.559 Hom.: 1506

Bravo AF: 0.714

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs244895; hg19: chr5-167959307;