5-177100576-G-T

Variant names:

• chr5-177100576-G-T
• rs6556301

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 0.332 in 151,896 control chromosomes in the GnomAD database, including 8,838 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 0.33 (8838 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.333 AC: 50474 AN: 151780 Hom.: 8835 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.332 AC: 50505 AN: 151896 Hom.: 8838 Cov.: 31 AF XY: 0.336 AC XY: 24969 AN XY: 74234

African (AFR) AF: 0.245 AC: 10147 AN: 41350

American (AMR) AF: 0.352 AC: 5380 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2723 AN: 5160

South Asian (SAS) AF: 0.402 AC: 1941 AN: 4832

European-Finnish (FIN) AF: 0.384 AC: 4056 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24080 AN: 67948

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.345 Hom.: 32151

Bravo AF: 0.326

Asia WGS AF: 0.391 AC: 1363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.50
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs6556301; hg19: chr5-176527577;