rs11660783

Variant names:

• chr18-60100403-T-C
• rs11660783

Your query was ambiguous. Multiple possible variants found:

• chr18-60100403-T-C
• chr18-60100403-T-G

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 0.125 in 152,136 control chromosomes in the GnomAD database, including 1,614 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 0.13 (1614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.125 AC: 19050 AN: 152018 Hom.: 1613 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.125 AC: 19043 AN: 152136 Hom.: 1614 Cov.: 32 AF XY: 0.123 AC XY: 9144 AN XY: 74392

African (AFR) AF: 0.0294 AC: 1221 AN: 41544

American (AMR) AF: 0.104 AC: 1593 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3466

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5170

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4826

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10610

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12321 AN: 67956

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.152 Hom.: 1980

Bravo AF: 0.114

Asia WGS AF: 0.0960 AC: 336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.88
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs11660783; hg19: chr18-57767635;