rs11665307

Variant names:

• chr18-71698064-T-C
• rs11665307

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 0.148 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
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.148 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

African (AFR) AF: 0.104 AC: 4312 AN: 41518

American (AMR) AF: 0.139 AC: 2122 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3470

East Asian (EAS) AF: 0.00175 AC: 9 AN: 5156

South Asian (SAS) AF: 0.108 AC: 520 AN: 4824

European-Finnish (FIN) AF: 0.236 AC: 2501 AN: 10576

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12177 AN: 67974

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.158 Hom.: 713

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11665307; hg19: chr18-69365300;