rs9957673

Variant names:

• chr18-59899156-C-T
• rs9957673

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 0.219 in 152,124 control chromosomes in the GnomAD database, including 4,527 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 0.22 (4527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.219 AC: 33298 AN: 152006 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.219 AC: 33346 AN: 152124 Hom.: 4527 Cov.: 32 AF XY: 0.218 AC XY: 16201 AN XY: 74382

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.0815

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.186

Alfa AF: 0.167 Hom.: 2369

Bravo AF: 0.217

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9957673; hg19: chr18-57566388;