5-119681605-T-C

Variant names:

• chr5-119681605-T-C
• rs330201

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 0.794 in 152,138 control chromosomes in the GnomAD database, including 48,525 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 0.79 (48525 hom., cov: 32)
• Consequence: LOC348958 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 publications found

Genes affected

LOC348958 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120701 AN: 152020 Hom.: 48472 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.794 AC: 120815 AN: 152138 Hom.: 48525 Cov.: 32 AF XY: 0.788 AC XY: 58624 AN XY: 74388

African (AFR) AF: 0.928 AC: 38530 AN: 41512

American (AMR) AF: 0.724 AC: 11062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4492 AN: 5182

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4822

European-Finnish (FIN) AF: 0.667 AC: 7050 AN: 10570

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50845 AN: 67988

Other (OTH) AF: 0.792 AC: 1671 AN: 2110

Alfa AF: 0.761 Hom.: 75156

Bravo AF: 0.804

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs330201; hg19: chr5-119017300;