rs17048403

Variant names:

• chr4-136030719-A-G
• rs17048403

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 0.162 in 152,144 control chromosomes in the GnomAD database, including 2,307 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 0.16 (2307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.162 AC: 24620 AN: 152024 Hom.: 2301 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.162 AC: 24659 AN: 152144 Hom.: 2307 Cov.: 32 AF XY: 0.162 AC XY: 12072 AN XY: 74384

African (AFR) AF: 0.259 AC: 10757 AN: 41490

American (AMR) AF: 0.148 AC: 2257 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3472

East Asian (EAS) AF: 0.0901 AC: 467 AN: 5184

South Asian (SAS) AF: 0.160 AC: 773 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1516 AN: 10580

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7796 AN: 67998

Other (OTH) AF: 0.156 AC: 329 AN: 2110

Alfa AF: 0.149 Hom.: 235

Bravo AF: 0.170

Asia WGS AF: 0.190 AC: 655 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs17048403; hg19: chr4-136951874;