5-119656288-C-T

Variant names:

• chr5-119656288-C-T
• rs330196

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 0.252 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.169 AC: 7018 AN: 41482

American (AMR) AF: 0.269 AC: 4104 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3468

East Asian (EAS) AF: 0.193 AC: 998 AN: 5176

South Asian (SAS) AF: 0.380 AC: 1830 AN: 4816

European-Finnish (FIN) AF: 0.307 AC: 3232 AN: 10536

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19561 AN: 67926

Other (OTH) AF: 0.241 AC: 509 AN: 2108

Alfa AF: 0.279 Hom.: 3239

Bravo AF: 0.239

Asia WGS AF: 0.286 AC: 993 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs330196; hg19: chr5-118991983;