18-69111089-T-C

Variant names:

• chr18-69111089-T-C
• rs3891810

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 0.187 in 151,916 control chromosomes in the GnomAD database, including 3,180 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 0.19 (3180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 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: 0.187 AC: 28380 AN: 151798 Hom.: 3175 Cov.: 32

Gnomad AFR AF: 0.0629

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.187 AC: 28390 AN: 151916 Hom.: 3180 Cov.: 32 AF XY: 0.190 AC XY: 14140 AN XY: 74244

African (AFR) AF: 0.0627 AC: 2607 AN: 41550

American (AMR) AF: 0.206 AC: 3122 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1201 AN: 5162

South Asian (SAS) AF: 0.289 AC: 1389 AN: 4814

European-Finnish (FIN) AF: 0.254 AC: 2686 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 15985 AN: 67840

Other (OTH) AF: 0.201 AC: 424 AN: 2106

Alfa AF: 0.209 Hom.: 5140

Bravo AF: 0.177

Asia WGS AF: 0.255 AC: 886 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs3891810; hg19: chr18-66778326; COSMIC: COSV107179366;