rs17048403

Variant names:

• chr4-136030719-A-G
• rs17048403

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0901

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.156

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17048403; hg19: chr4-136951874;