rs9961113

Variant names:

• chr18-77893443-T-C
• rs9961113

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 0.323 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.542 AC: 22480 AN: 41502

American (AMR) AF: 0.267 AC: 4087 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5164

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2097 AN: 10566

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15054 AN: 67982

Other (OTH) AF: 0.285 AC: 600 AN: 2106

Alfa AF: 0.253 Hom.: 9163

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
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs9961113; hg19: chr18-75605399;