rs4643387

Positions:

• chr17-18069659-T-C

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 0.579 in 152,100 control chromosomes in the GnomAD database, including 26,813 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 0.58 (26813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785

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 (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87998 AN: 151982 Hom.: 26791 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.579 AC: 88066 AN: 152100 Hom.: 26813 Cov.: 32 AF XY: 0.566 AC XY: 42097 AN XY: 74364

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.586

Alfa AF: 0.607 Hom.: 4965

Bravo AF: 0.572

Asia WGS AF: 0.277 AC: 968 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	5.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4643387; hg19: chr17-17972973;