chr5-121741879-T-C

Variant names:

• chr5-121741879-T-C
• rs1588260

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 0.247 in 151,976 control chromosomes in the GnomAD database, including 5,880 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 (5880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37544 AN: 151858 Hom.: 5857 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.247 AC: 37608 AN: 151976 Hom.: 5880 Cov.: 32 AF XY: 0.246 AC XY: 18276 AN XY: 74278

African (AFR) AF: 0.447 AC: 18513 AN: 41446

American (AMR) AF: 0.234 AC: 3566 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1065 AN: 5146

South Asian (SAS) AF: 0.204 AC: 974 AN: 4774

European-Finnish (FIN) AF: 0.178 AC: 1885 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10384 AN: 67992

Other (OTH) AF: 0.233 AC: 490 AN: 2100

Alfa AF: 0.111 Hom.: 220

Bravo AF: 0.265

Asia WGS AF: 0.222 AC: 771 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.56
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1588260; hg19: chr5-121077574;