rs17570669

chr4-110815726-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 0.0556 in 151,864 control chromosomes in the GnomAD database, including 324 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 0.056 (324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0789 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: 0.0557 AC: 8445 AN: 151746 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0556 AC: 8443 AN: 151864 Hom.: 324 Cov.: 32 AF XY: 0.0515 AC XY: 3826 AN XY: 74232

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0609 Hom.: 46

Bravo AF: 0.0560

Asia WGS AF: 0.0170 AC: 59 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.011
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17570669; hg19: chr4-111736882;