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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128121		n.144517014T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;