rs9961404

Positions:

• chr18-59210305-C-T

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 152,104 control chromosomes in the GnomAD database, including 2,443 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 (2443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 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: 0.173 AC: 26333 AN: 151986 Hom.: 2436 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.173 AC: 26353 AN: 152104 Hom.: 2443 Cov.: 32 AF XY: 0.179 AC XY: 13314 AN XY: 74330

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.180

Alfa AF: 0.170 Hom.: 3161

Bravo AF: 0.171

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9961404; hg19: chr18-56877537;