rs1603117

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;