chr5-161728308-C-G

Variant names:

• chr5-161728308-C-G
• rs4128400

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 0.632 in 151,892 control chromosomes in the GnomAD database, including 30,522 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 0.63 (30522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.632 AC: 95917 AN: 151774 Hom.: 30474 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.632 AC: 96019 AN: 151892 Hom.: 30522 Cov.: 32 AF XY: 0.637 AC XY: 47267 AN XY: 74222

African (AFR) AF: 0.617 AC: 25544 AN: 41420

American (AMR) AF: 0.699 AC: 10664 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3893 AN: 5168

South Asian (SAS) AF: 0.698 AC: 3352 AN: 4800

European-Finnish (FIN) AF: 0.641 AC: 6762 AN: 10544

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41710 AN: 67922

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.499 Hom.: 1356

Bravo AF: 0.636

Asia WGS AF: 0.750 AC: 2601 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0080
DANN	Benign	0.55
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4128400; hg19: chr5-161155314;