rs1603117

Variant names:

• chr4-69530227-G-A
• rs1603117

Your query was ambiguous. Multiple possible variants found:

• chr4-69530227-G-A
• chr4-69530227-G-C

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 0.588 in 151,964 control chromosomes in the GnomAD database, including 26,983 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 0.59 (26983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.588 AC: 89293 AN: 151846 Hom.: 26973 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.588 AC: 89345 AN: 151964 Hom.: 26983 Cov.: 31 AF XY: 0.595 AC XY: 44190 AN XY: 74274

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.602

Alfa AF: 0.627 Hom.: 43763

Bravo AF: 0.580

Asia WGS AF: 0.684 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1603117; hg19: chr4-70395945;