4-109904478-G-A

Variant names:

• chr4-109904478-G-A
• rs17316633

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 0.218 in 152,048 control chromosomes in the GnomAD database, including 3,726 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 0.22 (3726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 15 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 (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.218 AC: 33095 AN: 151930 Hom.: 3731 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.218 AC: 33094 AN: 152048 Hom.: 3726 Cov.: 32 AF XY: 0.214 AC XY: 15897 AN XY: 74320

African (AFR) AF: 0.176 AC: 7309 AN: 41454

American (AMR) AF: 0.203 AC: 3107 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3472

East Asian (EAS) AF: 0.0839 AC: 435 AN: 5186

South Asian (SAS) AF: 0.202 AC: 972 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10566

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17250 AN: 67964

Other (OTH) AF: 0.233 AC: 493 AN: 2114

Alfa AF: 0.240 Hom.: 17124

Bravo AF: 0.212

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs17316633; hg19: chr4-110825634;