rs11665646

Variant names:

• chr18-59925107-C-T
• rs11665646

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 0.129 in 152,260 control chromosomes in the GnomAD database, including 1,523 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 (1523 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 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: 0.130 AC: 19725 AN: 152142 Hom.: 1522 Cov.: 33

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.129 AC: 19716 AN: 152260 Hom.: 1523 Cov.: 33 AF XY: 0.129 AC XY: 9636 AN XY: 74442

African (AFR) AF: 0.0452 AC: 1880 AN: 41562

American (AMR) AF: 0.131 AC: 2010 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1205 AN: 5182

South Asian (SAS) AF: 0.161 AC: 775 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10588

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11316 AN: 68010

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.156 Hom.: 3285

Bravo AF: 0.125

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.73
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs11665646; hg19: chr18-57592339;