rs9961404

Variant names:

• chr18-59210305-C-T
• rs9961404

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;