rs17390445

chr4-34892233-A-Gchr4-34892233-A-T

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 0.597 in 151,808 control chromosomes in the GnomAD database, including 28,654 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 0.60 (28654 hom., cov: 31)
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90604 AN: 151690 Hom.: 28630 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.597 AC: 90668 AN: 151808 Hom.: 28654 Cov.: 31 AF XY: 0.604 AC XY: 44828 AN XY: 74202

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.604

Alfa AF: 0.661 Hom.: 39885

Bravo AF: 0.588

Asia WGS AF: 0.766 AC: 2651 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17390445; hg19: chr4-34893855;