4-170521145-T-A

Variant names:

• chr4-170521145-T-A
• rs1507699

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 0.0534 in 152,250 control chromosomes in the GnomAD database, including 290 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 0.053 (290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 8111 AN: 152132 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0474

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0254

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0534 AC: 8128 AN: 152250 Hom.: 290 Cov.: 32 AF XY: 0.0517 AC XY: 3846 AN XY: 74438

African (AFR) AF: 0.103 AC: 4259 AN: 41542

American (AMR) AF: 0.0501 AC: 765 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0474 AC: 164 AN: 3462

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0261 AC: 126 AN: 4830

European-Finnish (FIN) AF: 0.0252 AC: 267 AN: 10612

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2373 AN: 68012

Other (OTH) AF: 0.0549 AC: 116 AN: 2114

Alfa AF: 0.0482 Hom.: 32

Bravo AF: 0.0569

Asia WGS AF: 0.0160 AC: 55 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1507699; hg19: chr4-171442296;