rs11665307

chr18-71698064-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 0.148 in 152,070 control chromosomes in the GnomAD database, including 1,949 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 0.15 (1949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.148 AC: 22549 AN: 151950 Hom.: 1948 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.148 AC: 22559 AN: 152070 Hom.: 1949 Cov.: 32 AF XY: 0.150 AC XY: 11158 AN XY: 74324

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00175

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.118

Alfa AF: 0.162 Hom.: 577

Bravo AF: 0.141

Asia WGS AF: 0.0580 AC: 203 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.16
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11665307; hg19: chr18-69365300;