rs17600303

chr4-44515687-C-G

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 0.0356 in 151,778 control chromosomes in the GnomAD database, including 227 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 0.036 (227 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0853 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: 0.0355 AC: 5388 AN: 151660 Hom.: 229 Cov.: 30

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.00722

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00653

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0356 AC: 5397 AN: 151778 Hom.: 227 Cov.: 30 AF XY: 0.0372 AC XY: 2761 AN XY: 74142

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0874

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.00722

Gnomad4 NFE AF: 0.00653

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.0225 Hom.: 16

Bravo AF: 0.0380

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0070
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17600303; hg19: chr4-44517704;