rs669715

Variant names:

• chr11-107567725-T-C
• rs669715

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 0.439 in 151,962 control chromosomes in the GnomAD database, including 15,143 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 0.44 (15143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66615 AN: 151844 Hom.: 15119 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.439 AC: 66688 AN: 151962 Hom.: 15143 Cov.: 32 AF XY: 0.438 AC XY: 32537 AN XY: 74276

African (AFR) AF: 0.560 AC: 23225 AN: 41440

American (AMR) AF: 0.415 AC: 6340 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2110 AN: 5154

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4812

European-Finnish (FIN) AF: 0.385 AC: 4055 AN: 10536

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26513 AN: 67956

Other (OTH) AF: 0.412 AC: 867 AN: 2104

Alfa AF: 0.408 Hom.: 10560

Bravo AF: 0.446

Asia WGS AF: 0.444 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.54
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs669715; hg19: chr11-107438451;