chr5-68119886-C-T

Variant names:

• chr5-68119886-C-T
• rs9332463

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.249 AC: 10322 AN: 41450

American (AMR) AF: 0.423 AC: 6450 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 667 AN: 3464

East Asian (EAS) AF: 0.762 AC: 3934 AN: 5166

South Asian (SAS) AF: 0.376 AC: 1808 AN: 4812

European-Finnish (FIN) AF: 0.298 AC: 3149 AN: 10562

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24840 AN: 67962

Other (OTH) AF: 0.308 AC: 648 AN: 2106

Alfa AF: 0.341 Hom.: 1210

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

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