5-68119886-C-T

Position:

• chr5-68119886-C-T

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 0.343 in 151,984 control chromosomes in the GnomAD database, including 9,837 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 0.34 (9837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.343 AC: 52120 AN: 151866 Hom.: 9817 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.343 AC: 52163 AN: 151984 Hom.: 9837 Cov.: 32 AF XY: 0.344 AC XY: 25562 AN XY: 74292

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.308

Alfa AF: 0.345 Hom.: 1187

Bravo AF: 0.349

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332463; hg19: chr5-67415714; COSMIC: COSV60150558;