rs4643387

Variant names:

• chr17-18069659-T-C
• rs4643387

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 0.579 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
• Publications: 11 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.534 AC: 22147 AN: 41464

American (AMR) AF: 0.498 AC: 7603 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5188

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4822

European-Finnish (FIN) AF: 0.594 AC: 6279 AN: 10568

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46153 AN: 67992

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

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
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs4643387; hg19: chr17-17972973;