4-160107665-A-G

Variant names:

• chr4-160107665-A-G
• rs17261688

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 0.0915 in 152,272 control chromosomes in the GnomAD database, including 874 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 0.092 (874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.137 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: 0.0916 AC: 13945 AN: 152156 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0915 AC: 13938 AN: 152272 Hom.: 874 Cov.: 32 AF XY: 0.0869 AC XY: 6472 AN XY: 74462

African (AFR) AF: 0.0233 AC: 970 AN: 41572

American (AMR) AF: 0.0927 AC: 1417 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0558 AC: 269 AN: 4824

European-Finnish (FIN) AF: 0.0743 AC: 789 AN: 10614

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9444 AN: 67996

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.132 Hom.: 1682

Bravo AF: 0.0900

Asia WGS AF: 0.0250 AC: 86 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs17261688; hg19: chr4-161028817;