rs17570669

Variant names:

• chr4-110815726-A-T
• rs17570669

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0145 AC: 604 AN: 41522

American (AMR) AF: 0.0649 AC: 986 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 452 AN: 3458

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5142

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4822

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5471 AN: 67812

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17570669; hg19: chr4-111736882;