chr5-119656288-C-T

Variant names:

• chr5-119656288-C-T
• rs330196

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 0.252 in 151,972 control chromosomes in the GnomAD database, including 5,077 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 0.25 (5077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.252 AC: 38317 AN: 151854 Hom.: 5077 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.252 AC: 38330 AN: 151972 Hom.: 5077 Cov.: 32 AF XY: 0.258 AC XY: 19143 AN XY: 74262

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.241

Alfa AF: 0.279 Hom.: 2936

Bravo AF: 0.239

Asia WGS AF: 0.286 AC: 993 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs330196; hg19: chr5-118991983;