rs4575595

chr17-63499854-G-A

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 0.433 in 152,158 control chromosomes in the GnomAD database, including 15,051 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 0.43 (15051 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 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: 0.433 AC: 65814 AN: 152042 Hom.: 15024 Cov.: 34

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.433 AC: 65855 AN: 152158 Hom.: 15051 Cov.: 34 AF XY: 0.437 AC XY: 32506 AN XY: 74384

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.409

Alfa AF: 0.457 Hom.: 2046

Bravo AF: 0.422

Asia WGS AF: 0.617 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.1
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4575595; hg19: chr17-61577215;