4-188199757-T-C

Variant names:

• chr4-188199757-T-C
• rs6857559

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 0.631 in 152,022 control chromosomes in the GnomAD database, including 30,787 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 (30787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95873 AN: 151904 Hom.: 30760 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.631 AC: 95950 AN: 152022 Hom.: 30787 Cov.: 32 AF XY: 0.634 AC XY: 47099 AN XY: 74294

African (AFR) AF: 0.629 AC: 26072 AN: 41476

American (AMR) AF: 0.600 AC: 9169 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3466

East Asian (EAS) AF: 0.989 AC: 5097 AN: 5152

South Asian (SAS) AF: 0.780 AC: 3762 AN: 4820

European-Finnish (FIN) AF: 0.593 AC: 6253 AN: 10550

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41588 AN: 67968

Other (OTH) AF: 0.636 AC: 1346 AN: 2116

Alfa AF: 0.616 Hom.: 94910

Bravo AF: 0.630

Asia WGS AF: 0.877 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.5
DANN	Benign	0.47
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6857559; hg19: chr4-189120911;