rs9963878

Variant names:

• chr18-51153152-T-C
• rs9963878

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 0.173 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.388 AC: 16080 AN: 41468

American (AMR) AF: 0.110 AC: 1681 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.162 AC: 841 AN: 5176

South Asian (SAS) AF: 0.116 AC: 558 AN: 4820

European-Finnish (FIN) AF: 0.0646 AC: 684 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0843 AC: 5735 AN: 67996

Other (OTH) AF: 0.153 AC: 322 AN: 2108

Alfa AF: 0.191 Hom.: 1343

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs9963878; hg19: chr18-48679522;