5-68318567-G-C

Variant names:

• chr5-68318567-G-C
• rs256508

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 0.382 in 152,010 control chromosomes in the GnomAD database, including 12,611 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 0.38 (12611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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: 0.382 AC: 58071 AN: 151892 Hom.: 12619 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.382 AC: 58060 AN: 152010 Hom.: 12611 Cov.: 32 AF XY: 0.385 AC XY: 28607 AN XY: 74276

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.405

Alfa AF: 0.424 Hom.: 1799

Bravo AF: 0.363

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	8.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs256508; hg19: chr5-67614395;