rs9963878

chr18-51153152-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 0.173 in 152,112 control chromosomes in the GnomAD database, including 3,664 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 0.17 (3664 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 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: 0.172 AC: 26210 AN: 151994 Hom.: 3658 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.173 AC: 26263 AN: 152112 Hom.: 3664 Cov.: 33 AF XY: 0.168 AC XY: 12523 AN XY: 74368

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0646

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.153

Alfa AF: 0.121 Hom.: 389

Bravo AF: 0.185

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9963878; hg19: chr18-48679522;