rs1198186

Variant names:

• chr5-144517014-T-C
• rs358655

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 0.275 in 151,984 control chromosomes in the GnomAD database, including 6,067 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 0.27 (6067 hom., cov: 31)
• Consequence: LOC100128121 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 publications found

Genes affected

LOC100128121 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 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: 0.275 AC: 41739 AN: 151866 Hom.: 6071 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.275 AC: 41734 AN: 151984 Hom.: 6067 Cov.: 31 AF XY: 0.272 AC XY: 20175 AN XY: 74278

African (AFR) AF: 0.304 AC: 12574 AN: 41400

American (AMR) AF: 0.188 AC: 2870 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.0698 AC: 361 AN: 5174

South Asian (SAS) AF: 0.423 AC: 2024 AN: 4790

European-Finnish (FIN) AF: 0.253 AC: 2682 AN: 10584

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19407 AN: 67980

Other (OTH) AF: 0.286 AC: 604 AN: 2110

Alfa AF: 0.276 Hom.: 737

Bravo AF: 0.265

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.49

Splicing

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

Other links and lift over

dbSNP: rs358655; hg19: chr5-143896577;