rs9961113

chr18-77893443-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 0.323 in 152,102 control chromosomes in the GnomAD database, including 9,467 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 0.32 (9467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 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: 0.323 AC: 49077 AN: 151986 Hom.: 9438 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.323 AC: 49162 AN: 152102 Hom.: 9467 Cov.: 32 AF XY: 0.323 AC XY: 24032 AN XY: 74352

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.285

Alfa AF: 0.246 Hom.: 4576

Bravo AF: 0.332

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.031
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9961113; hg19: chr18-75605399;